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Richter F, Calonne-Salmon M, van der Heijden MGA, Declerck S, Stanley CE. AMF-SporeChip provides new insights into arbuscular mycorrhizal fungal asymbiotic hyphal growth dynamics at the cellular level. LAB ON A CHIP 2024; 24:1930-1946. [PMID: 38416560 DOI: 10.1039/d3lc00859b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Arbuscular mycorrhizal fungi (AMF) form symbiotic associations with the majority of land plants and deliver a wide range of soil-based ecosystem services. Due to their conspicuous belowground lifestyle in a dark environment surrounded by soil particles, much is still to be learned about the influence of environmental (i.e., physical) cues on spore germination, hyphal morphogenesis and anastomosis/hyphal healing mechanisms. To fill existing gaps in AMF knowledge, we developed a new microfluidic platform - the AMF-SporeChip - to visualise the foraging behaviour of germinating Rhizophagus and Gigaspora spores and confront asymbiotic hyphae with physical obstacles. In combination with timelapse microscopy, the fungi could be examined at the cellular level and in real-time. The AMF-SporeChip allowed us to acquire movies with unprecedented visual clarity and therefore identify various exploration strategies of AMF asymbiotic hyphae. We witnessed tip-to-tip and tip-to-side hyphal anastomosis formation. Anastomosis involved directed hyphal growth in a "stop-and-go" manner, yielding visual evidence of pre-anastomosis signalling and decision-making. Remarkably, we also revealed a so-far undescribed reversible cytoplasmic retraction, including the formation of up to 8 septa upon retraction, as part of a highly dynamic space navigation, probably evolved to optimise foraging efficiency. Our findings demonstrated how AMF employ an intricate mechanism of space searching, involving reversible cytoplasmic retraction, branching and directional changes. In turn, the AMF-SporeChip is expected to open many future frontiers for AMF research.
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Affiliation(s)
- Felix Richter
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
| | - Maryline Calonne-Salmon
- Laboratory of Mycology, Earth and Life Institute, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
| | - Marcel G A van der Heijden
- Agroecology and Environment Research Division, Agroscope, 8046 Zurich, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland
- Institute of Environmental Biology, Utrecht University, 3584 CS Utrecht, The Netherlands
| | - Stéphane Declerck
- Laboratory of Mycology, Earth and Life Institute, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
| | - Claire E Stanley
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
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2
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Földi C, Merényi Z, Balázs B, Csernetics Á, Miklovics N, Wu H, Hegedüs B, Virágh M, Hou Z, Liu XB, Galgóczy L, Nagy LG. Snowball: a novel gene family required for developmental patterning of fruiting bodies of mushroom-forming fungi (Agaricomycetes). mSystems 2024; 9:e0120823. [PMID: 38334416 PMCID: PMC10949477 DOI: 10.1128/msystems.01208-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/10/2024] [Indexed: 02/10/2024] Open
Abstract
The morphogenesis of sexual fruiting bodies of fungi is a complex process determined by a genetically encoded program. Fruiting bodies reached the highest complexity levels in the Agaricomycetes; yet, the underlying genetics is currently poorly known. In this work, we functionally characterized a highly conserved gene termed snb1, whose expression level increases rapidly during fruiting body initiation. According to phylogenetic analyses, orthologs of snb1 are present in almost all agaricomycetes and may represent a novel conserved gene family that plays a substantial role in fruiting body development. We disrupted snb1 using CRISPR/Cas9 in the agaricomycete model organism Coprinopsis cinerea. snb1 deletion mutants formed unique, snowball-shaped, rudimentary fruiting bodies that could not differentiate caps, stipes, and lamellae. We took advantage of this phenotype to study fruiting body differentiation using RNA-Seq analyses. This revealed differentially regulated genes and gene families that, based on wild-type RNA-Seq data, were upregulated early during development and showed tissue-specific expression, suggesting a potential role in differentiation. Taken together, the novel gene family of snb1 and the differentially expressed genes in the snb1 mutants provide valuable insights into the complex mechanisms underlying developmental patterning in the Agaricomycetes. IMPORTANCE Fruiting bodies of mushroom-forming fungi (Agaricomycetes) are complex multicellular structures, with a spatially and temporally integrated developmental program that is, however, currently poorly known. In this study, we present a novel, conserved gene family, Snowball (snb), termed after the unique, differentiation-less fruiting body morphology of snb1 knockout strains in the model mushroom Coprinopsis cinerea. snb is a gene of unknown function that is highly conserved among agaricomycetes and encodes a protein of unknown function. A comparative transcriptomic analysis of the early developmental stages of differentiated wild-type and non-differentiated mutant fruiting bodies revealed conserved differentially expressed genes which may be related to tissue differentiation and developmental patterning fruiting body development.
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Affiliation(s)
- Csenge Földi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - Zsolt Merényi
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
| | - Bálint Balázs
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
| | - Árpád Csernetics
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
| | - Nikolett Miklovics
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
| | - Hongli Wu
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
| | - Botond Hegedüs
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
| | - Máté Virágh
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
| | - Zhihao Hou
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
| | - Xiao-Bin Liu
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
| | - László Galgóczy
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
- Department of Biotechnology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary
| | - László G. Nagy
- Synthetic and Systems Biology Unit, Institute of Biochemistry, HUN-REN Biological Research Center, Szeged, Hungary
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3
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Arellano-Caicedo C, Beech JP, Bengtsson M, Ohlsson P, Hammer EC. Quantification of growth and nutrient consumption of bacterial and fungal cultures in microfluidic microhabitat models. STAR Protoc 2024; 5:102784. [PMID: 38103191 PMCID: PMC10783617 DOI: 10.1016/j.xpro.2023.102784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/07/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
Understanding microbes in nature requires consideration of their microenvironment. Here, we present a protocol for quantifying biomass and nutrient degradation of bacterial and fungal cultures (Pseudomonas putida and Coprinopsis cinerea, respectively) in microfluidics. We describe steps for mask design and fabrication, master printing, polydimethylsiloxane chip fabrication, and chip inoculation and imaging using fluorescence microscopy. We include procedures for image analysis, plotting, and statistics. For complete details on the use and execution of this protocol, please refer to Arellano-Caicedo et al. (2023).1.
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Affiliation(s)
- Carlos Arellano-Caicedo
- Center of Microbiology and Environmental System Sciences, University of Vienna, 1030 Vienna, Austria; Department of Biology, Lund University, 22362 Lund, Sweden.
| | - Jason P Beech
- Division of Solid-State Physics, Lund University, 22363 Lund, Sweden
| | - Martin Bengtsson
- Department of Biomedical Engineering, Lund University, 22363 Lund, Sweden
| | - Pelle Ohlsson
- Department of Biomedical Engineering, Lund University, 22363 Lund, Sweden
| | - Edith C Hammer
- Department of Biology, Lund University, 22362 Lund, Sweden.
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4
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Ugolini GS, Wang M, Secchi E, Pioli R, Ackermann M, Stocker R. Microfluidic approaches in microbial ecology. LAB ON A CHIP 2024; 24:1394-1418. [PMID: 38344937 PMCID: PMC10898419 DOI: 10.1039/d3lc00784g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Microbial life is at the heart of many diverse environments and regulates most natural processes, from the functioning of animal organs to the cycling of global carbon. Yet, the study of microbial ecology is often limited by challenges in visualizing microbial processes and replicating the environmental conditions under which they unfold. Microfluidics operates at the characteristic scale at which microorganisms live and perform their functions, thus allowing for the observation and quantification of behaviors such as growth, motility, and responses to external cues, often with greater detail than classical techniques. By enabling a high degree of control in space and time of environmental conditions such as nutrient gradients, pH levels, and fluid flow patterns, microfluidics further provides the opportunity to study microbial processes in conditions that mimic the natural settings harboring microbial life. In this review, we describe how recent applications of microfluidic systems to microbial ecology have enriched our understanding of microbial life and microbial communities. We highlight discoveries enabled by microfluidic approaches ranging from single-cell behaviors to the functioning of multi-cellular communities, and we indicate potential future opportunities to use microfluidics to further advance our understanding of microbial processes and their implications.
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Affiliation(s)
- Giovanni Stefano Ugolini
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Miaoxiao Wang
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland
| | - Eleonora Secchi
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Roberto Pioli
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
| | - Martin Ackermann
- Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Duebendorf, Switzerland
- Laboratory of Microbial Systems Ecology, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédéral de Lausanne (EPFL), Lausanne, Switzerland
| | - Roman Stocker
- Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, ETH Zurich, Laura-Hezner-Weg 7, 8093 Zurich, Switzerland.
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5
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Mafla-Endara PM, Meklesh V, Beech JP, Ohlsson P, Pucetaite M, Hammer EC. Exposure to polystyrene nanoplastics reduces bacterial and fungal biomass in microfabricated soil models. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166503. [PMID: 37633381 DOI: 10.1016/j.scitotenv.2023.166503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/04/2023] [Accepted: 08/21/2023] [Indexed: 08/28/2023]
Abstract
Nanoplastics have been proven to induce toxicity in diverse organisms, yet their effect on soil microbes like bacteria and fungi remains largely unexplored. In this paper, we used micro-engineered soil models to investigate the effect of polystyrene (PS) nanospheres on Pseudomonas putida and Coprinopsis cinerea. Specifically, we explored the effects of increasing concentrations of 60 nm carboxylated bovine serum albumin (BSA) coated nanospheres (0, 0.5, 2, and 10 mg/L) on these bacterial and fungal model organisms respectively, over time. We found that both microorganisms could disperse through the PS solution, but long-distance dispersal was reduced by high concentrations. Microbial biomass decreased in all treatments, in which bacteria showed a linear dose response with the strongest effect at 10 mg/L concentration, and fungi showed a non-linear response with the strongest effect at 2 mg/L concentration. At the highest nanoplastics concentration, the first colonizing fungal hyphae adsorbed most of the PS nanospheres present in their vicinity, in a process that we termed the 'vacuum cleaner effect'. As a result, the toxicity effect of the original treatment on subsequently growing fungal hyphae was reduced to a growth level indistinguishable from the control. We did not find evidence that nanoplastics are able to penetrate bacterial nor fungal cell walls. Overall, our findings provide evidence that nanoplastics can cause a direct negative effect on soil microbes and highlight the need for further studies that can explain how the microbial stress response might affect soil functions.
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Affiliation(s)
- Paola M Mafla-Endara
- Centre for Environmental and Climate Science (CEC), Lund University, Lund, Sweden; Department of Biology, Lund University, Lund, Sweden.
| | - Viktoriia Meklesh
- Centre for Environmental and Climate Science (CEC), Lund University, Lund, Sweden; Physical Chemistry Division, Department of Chemistry, Lund University, Lund, Sweden
| | - Jason P Beech
- Division of Solid State Physics, Department of Physics and NanoLund, Lund University, Lund, Sweden
| | - Pelle Ohlsson
- Department of Biomedical Engineering, Faculty of Engineering (LTH), Lund University, Lund, Sweden
| | | | - Edith C Hammer
- Centre for Environmental and Climate Science (CEC), Lund University, Lund, Sweden; Department of Biology, Lund University, Lund, Sweden
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6
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Alonso Baez L, Bacete L. Cell wall dynamics: novel tools and research questions. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6448-6467. [PMID: 37539735 PMCID: PMC10662238 DOI: 10.1093/jxb/erad310] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 08/02/2023] [Indexed: 08/05/2023]
Abstract
Years ago, a classic textbook would define plant cell walls based on passive features. For instance, a sort of plant exoskeleton of invariable polysaccharide composition, and probably painted in green. However, currently, this view has been expanded to consider plant cell walls as active, heterogeneous, and dynamic structures with a high degree of complexity. However, what do we mean when we refer to a cell wall as a dynamic structure? How can we investigate the different implications of this dynamism? While the first question has been the subject of several recent publications, defining the ideal strategies and tools needed to address the second question has proven to be challenging due to the myriad of techniques available. In this review, we will describe the capacities of several methodologies to study cell wall composition, structure, and other aspects developed or optimized in recent years. Keeping in mind cell wall dynamism and plasticity, the advantages of performing long-term non-invasive live-imaging methods will be emphasized. We specifically focus on techniques developed for Arabidopsis thaliana primary cell walls, but the techniques could be applied to both secondary cell walls and other plant species. We believe this toolset will help researchers in expanding knowledge of these dynamic/evolving structures.
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Affiliation(s)
- Luis Alonso Baez
- Institute for Biology, Faculty of Natural Sciences, Norwegian University of Science and Technology, 5 Høgskoleringen, Trondheim, 7491, Norway
| | - Laura Bacete
- Institute for Biology, Faculty of Natural Sciences, Norwegian University of Science and Technology, 5 Høgskoleringen, Trondheim, 7491, Norway
- Umeå Plant Science Centre (UPSC), Department of Plant Physiology, Umeå University, 901 87 Umeå, Sweden
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7
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Maqsood Q, Sumrin A, Waseem R, Hussain M, Imtiaz M, Hussain N. Bioengineered microbial strains for detoxification of toxic environmental pollutants. ENVIRONMENTAL RESEARCH 2023; 227:115665. [PMID: 36907340 DOI: 10.1016/j.envres.2023.115665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/05/2023] [Accepted: 03/08/2023] [Indexed: 05/08/2023]
Abstract
Industrialization and other anthropogenic human activities pose significant environmental risks. As a result of the hazardous pollution, numerous living organisms may suffer from undesirable diseases in their separate habitats. Bioremediation, which removes hazardous compounds from the environment using microbes or their biologically active metabolites, is one of the most successful remediation approaches. According to the United Nations Environment Program (UNEP), deteriorating soil health negatively impacts food security and human health over time. Soil health restoration is critical right now. Microbes are widely known for their importance in cleaning up toxins present in the soil, such as heavy metals, pesticides, and hydrocarbons. However, the capacity of local bacteria to digest these pollutants is limited, and the process takes an extended time. Genetically modified organisms (GMOs), whose altered metabolic pathways promote the over-secretion of a variety of proteins favorable to the bioremediation process, can speed up the breakdown process. The need for remediation procedures, degrees of soil contamination, site circumstances, broad adoptions, and numerous possibilities occurring at various cleaning stages are all studied in detail. Massive efforts to restore contaminated soils have also resulted in severe issues. This review focuses on the enzymatic removal of hazardous pollutants from the environment, such as pesticides, heavy metals, dyes, and plastics. There are also in-depth assessments of present discoveries and future plans for efficient enzymatic degradation of hazardous pollutants.
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Affiliation(s)
- Quratulain Maqsood
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Aleena Sumrin
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Rafia Waseem
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Maria Hussain
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Mehwish Imtiaz
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Nazim Hussain
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan.
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8
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Richter I, Wein P, Uzum Z, Stanley CE, Krabbe J, Molloy EM, Moebius N, Ferling I, Hillmann F, Hertweck C. Transcription activator-like effector protects bacterial endosymbionts from entrapment within fungal hyphae. Curr Biol 2023:S0960-9822(23)00623-1. [PMID: 37301202 DOI: 10.1016/j.cub.2023.05.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/30/2023] [Accepted: 05/12/2023] [Indexed: 06/12/2023]
Abstract
As an endosymbiont of the ecologically and medically relevant fungus Rhizopus microsporus, the toxin-producing bacterium Mycetohabitans rhizoxinica faces myriad challenges, such as evading the host's defense mechanisms. However, the bacterial effector(s) that facilitate the remarkable ability of M. rhizoxinica to freely migrate within fungal hyphae have thus far remained unknown. Here, we show that a transcription activator-like (TAL) effector released by endobacteria is an essential symbiosis factor. By combining microfluidics with fluorescence microscopy, we observed enrichment of TAL-deficient M. rhizoxinica in side hyphae. High-resolution live imaging showed the formation of septa at the base of infected hyphae, leading to the entrapment of endobacteria. Using a LIVE/DEAD stain, we demonstrate that the intracellular survival of trapped TAL-deficient bacteria is significantly reduced compared with wild-type M. rhizoxinica, indicative of a protective host response in the absence of TAL proteins. Subversion of host defense in TAL-competent endobacteria represents an unprecedented function of TAL effectors. Our data illustrate an unusual survival strategy of endosymbionts in the host and provide deeper insights into the dynamic interactions between bacteria and eukaryotes.
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Affiliation(s)
- Ingrid Richter
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Philipp Wein
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Zerrin Uzum
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Claire E Stanley
- Department of Bioengineering, Imperial College, South Kensington, London SW7 2AZ, UK
| | - Jana Krabbe
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Evelyn M Molloy
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Nadine Moebius
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Iuliia Ferling
- Junior Research Group Evolution of Microbial Interactions, Leibniz Institute for Natural Product Research and Infection Biology, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Falk Hillmann
- Junior Research Group Evolution of Microbial Interactions, Leibniz Institute for Natural Product Research and Infection Biology, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany; Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany.
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9
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Arellano-Caicedo C, Ohlsson P, Bengtsson M, Beech JP, Hammer EC. Habitat complexity affects microbial growth in fractal maze. Curr Biol 2023; 33:1448-1458.e4. [PMID: 36933553 DOI: 10.1016/j.cub.2023.02.064] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 01/09/2023] [Accepted: 02/21/2023] [Indexed: 03/19/2023]
Abstract
The great variety of earth's microorganisms and their functions are attributed to the heterogeneity of their habitats, but our understanding of the impact of this heterogeneity on microbes is limited at the microscale. In this study, we tested how a gradient of spatial habitat complexity in the form of fractal mazes influenced the growth, substrate degradation, and interactions of the bacterial strain Pseudomonas putida and the fungal strain Coprinopsis cinerea. These strains responded in opposite ways: complex habitats strongly reduced fungal growth but, in contrast, increased the abundance of bacteria. Fungal hyphae did not reach far into the mazes and forced bacteria to grow in deeper regions. Bacterial substrate degradation strongly increased with habitat complexity, even more than bacterial biomass, up to an optimal depth, while the most remote parts of the mazes showed both decreased biomass and substrate degradation. These results suggest an increase in enzymatic activity in confined spaces, where areas may experience enhanced microbial activity and resource use efficiency. Very remote spaces showing a slower turnover of substrates illustrate a mechanism which may contribute to the long-term storage of organic matter in soils. We demonstrate here that the sole effect of spatial microstructures affects microbial growth and substrate degradation, leading to differences in local microscale spatial availability. These differences might add up to considerable changes in nutrient cycling at the macroscale, such as contributing to soil organic carbon storage.
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Affiliation(s)
| | - Pelle Ohlsson
- Department of Biomedical Engineering, Lund University, Ole Römers väg 3, 223 63 Lund, Sweden
| | - Martin Bengtsson
- Department of Biomedical Engineering, Lund University, Ole Römers väg 3, 223 63 Lund, Sweden
| | - Jason P Beech
- Division of Solid State Physics, Lund University, Sölvegatan 16, 223 63 Lund, Sweden
| | - Edith C Hammer
- Department of Biology, Lund University, Sölvegatan 35, 223 62 Lund, Sweden; Centre for Environmental and Climate Science, CEC, Lund University, Sölvegatan 37, 223 62 Lund, Sweden
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10
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Microbiome engineering for bioremediation of emerging pollutants. Bioprocess Biosyst Eng 2023; 46:323-339. [PMID: 36029349 DOI: 10.1007/s00449-022-02777-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/12/2022] [Indexed: 11/02/2022]
Abstract
Axenic microbial applications in the open environment are unrealistic and may not be always practically viable. Therefore, it is important to use mixed microbial cultures and their interactions with the microbiome in the targeted ecosystem to perform robust functions towards their sustainability in harsh environmental conditions. Emerging pollutants like phthalates and hydrocarbons that are toxic to several aquatic and terrestrial life forms in the water bodies and lands are an alarming situation. The present review explores the possibility of devising an inclusive eco-friendly strategy like microbiome engineering which proves to be a unique and crucial technology involving the power of microbial communication through quorum sensing. This review discusses the interspecies and intra-species communications between different microbial groups with their respective environments. Moreover, this review also envisages the efforts for designing the next level of microbiome-host engineering concept (MHEC). The focus of the review also extended toward using omics and metabolic network analysis-based tools for effective microbiome engineering. These approaches might be quite helpful in the future to understand such microbial interactions but it will be challenging to implement in the real environment to get the desired functions. Finally, the review also discusses multiple approaches for the bioremediation of toxic chemicals from the soil environment.
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11
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Pareek M, Hegedüs B, Hou Z, Csernetics Á, Wu H, Virágh M, Sahu N, Liu XB, Nagy L. Preassembled Cas9 Ribonucleoprotein-Mediated Gene Deletion Identifies the Carbon Catabolite Repressor and Its Target Genes in Coprinopsis cinerea. Appl Environ Microbiol 2022; 88:e0094022. [PMID: 36374019 PMCID: PMC9746306 DOI: 10.1128/aem.00940-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/11/2022] [Indexed: 11/16/2022] Open
Abstract
Cre1 is an important transcription factor that regulates carbon catabolite repression (CCR) and is widely conserved across fungi. The cre1 gene has been extensively studied in several Ascomycota species, whereas its role in gene expression regulation in the Basidiomycota species remains poorly understood. Here, we identified and investigated the role of cre1 in Coprinopsis cinerea, a basidiomycete model mushroom that can efficiently degrade lignocellulosic plant wastes. We used a rapid and efficient gene deletion approach based on PCR-amplified split-marker DNA cassettes together with in vitro assembled Cas9-guide RNA ribonucleoproteins (Cas9 RNPs) to generate C. cinerea cre1 gene deletion strains. Gene expression profiling of two independent C. cinerea cre1 mutants showed significant deregulation of carbohydrate metabolism, plant cell wall degrading enzymes (PCWDEs), plasma membrane transporter-related and several transcription factor-encoding genes, among others. Our results support the notion that, like reports in the ascomycetes, Cre1 of C. cinerea orchestrates CCR through a combined regulation of diverse genes, including PCWDEs, transcription factors that positively regulate PCWDEs, and membrane transporters which could import simple sugars that can induce the expression of PWCDEs. Somewhat paradoxically, though in accordance with other Agaricomycetes, genes related to lignin degradation were mostly downregulated in cre1 mutants, indicating they fall under different regulation than other PCWDEs. The gene deletion approach and the data presented here will expand our knowledge of CCR in the Basidiomycota and provide functional hypotheses on genes related to plant biomass degradation. IMPORTANCE Mushroom-forming fungi include some of the most efficient lignocellulosic plant biomass degraders. They degrade dead plant materials by a battery of lignin-, cellulose-, hemicellulose-, and pectin-degrading enzymes, the encoding genes of which are under tight transcriptional control. One of the highest-level regulations of these metabolic enzymes is known as carbon catabolite repression, which is orchestrated by the transcription factor Cre1, and ensures that costly lignocellulose-degrading enzyme genes are expressed only when simple carbon sources (e.g., glucose) are not available. Here, we identified the Cre1 ortholog in a litter decomposer Agaricomycete, Coprinopsis cinerea, knocked it out, and characterized transcriptional changes in the mutants. We identified several dozen lignocellulolytic enzyme genes as well as membrane transporters and other transcription factors as putative target genes of C. cinerea cre1. These results extend knowledge on carbon catabolite repression to litter decomposer Basidiomycota.
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Affiliation(s)
- Manish Pareek
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Botond Hegedüs
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Zhihao Hou
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Árpád Csernetics
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Hongli Wu
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Máté Virágh
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Neha Sahu
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - Xiao-Bin Liu
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
| | - László Nagy
- Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
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12
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Pham LHP, Colon-Ascanio M, Ou J, Ly K, Hu P, Choy JS, Luo X. Probing mutual interactions between Pseudomonas aeruginosa and Candida albicans in a biofabricated membrane-based microfluidic platform. LAB ON A CHIP 2022; 22:4349-4358. [PMID: 36239125 PMCID: PMC9756269 DOI: 10.1039/d2lc00728b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Microbes are typically found in multi-species (polymicrobial) communities. Cooperative and competitive interactions between species, mediated by diffusible factors and physical contact, leads to highly dynamic communities that undergo changes in composition diversity and size. Infections can be more severe or more difficult to treat when caused by multiple species. Interactions between species can improve the ability of one or more species to tolerate anti-microbial treatments and host defenses. Pseudomonas aeruginosa (Pa), a ubiquitous bacterium, and the opportunistic pathogenic yeast, Candida albicans (Ca), are frequently found together in cystic fibrosis lung infections and wound infections. While significant progress has been made in determining interactions between Pa and Ca, there are still important questions that remain unanswered. Here, we probe the mutual interactions between Pa and Ca in a custom-made microfluidic device using biopolymer chitosan membranes that support cross-species communication. By assembling microbes in physically separated, chemically communicating populations or bringing into direct interactions in a mixed culture, in situ polymicrobial growth and biofilm morphology were qualitatively characterized and quantified. Our work reveals new dynamic details of their mutual interactions including cooperation, competition, invasion, and biofilm formation. The membrane-based microfluidic platform can be further developed to understand the polymicrobial interactions within a controlled interactive microenvironment to improve microbial infection prevention and treatment.
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Affiliation(s)
- Le Hoang Phu Pham
- Department of Mechanical Engineering, School of Engineering, The Catholic University of America, Washington, DC 20064, USA.
| | - Mariliz Colon-Ascanio
- Department of Biology, School of Arts and Sciences, The Catholic University of America, Washington, DC 20064, USA.
| | - Jin Ou
- Department of Biology, School of Arts and Sciences, The Catholic University of America, Washington, DC 20064, USA.
| | - Khanh Ly
- Department of Biomedical Engineering, School of Engineering, The Catholic University of America, Washington, DC 20064, USA
| | - Piao Hu
- Department of Mechanical Engineering, School of Engineering, The Catholic University of America, Washington, DC 20064, USA.
| | - John S Choy
- Department of Biology, School of Arts and Sciences, The Catholic University of America, Washington, DC 20064, USA.
| | - Xiaolong Luo
- Department of Mechanical Engineering, School of Engineering, The Catholic University of America, Washington, DC 20064, USA.
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13
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Balseiro-Romero M, Prieto-Fernández Á, Shor LM, Ghoshal S, Baveye PC, Ortega-Calvo JJ. Chemotactic Bacteria Facilitate the Dispersion of Nonmotile Bacteria through Micrometer-Sized Pores in Engineered Porous Media. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:13975-13984. [PMID: 36103595 PMCID: PMC9535858 DOI: 10.1021/acs.est.2c03149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/09/2022] [Accepted: 08/20/2022] [Indexed: 06/15/2023]
Abstract
Recent research has demonstrated that chemotactic bacteria can disperse inside microsized pores while traveling toward favorable conditions. Microbe-microbe cotransport might enable nonmotile bacteria to be carried with motile partners to enhance their dispersion and reduce their deposition in porous systems. The aim of this study was to demonstrate the enhancement in the dispersion of nonmotile bacteria (Mycobacterium gilvum VM552, a polycyclic aromatic hydrocarbon-degrader, and Sphingobium sp. D4, a hexachlorocyclohexane-degrader, through micrometer-sized pores near the exclusion-cell-size limit, in the presence of motile Pseudomonas putida G7 cells. For this purpose, we used bioreactors equipped with two chambers that were separated with membrane filters with 3, 5, and 12 μm pore sizes and capillary polydimethylsiloxane (PDMS) microarrays (20 μm × 35 μm × 2.2 mm). The cotransport of nonmotile bacteria occurred exclusively in the presence of a chemoattractant concentration gradient, and therefore, a directed flow of motile cells. This cotransport was more intense in the presence of larger pores (12 μm) and strong chemoeffectors (γ-aminobutyric acid). The mechanism that governed cotransport at the cell scale involved mechanical pushing and hydrodynamic interactions. Chemotaxis-mediated cotransport of bacterial degraders and its implications in pore accessibility opens new avenues for the enhancement of bacterial dispersion in porous media and the biodegradation of heterogeneously contaminated scenarios.
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Affiliation(s)
- María Balseiro-Romero
- Instituto
de Recursos Naturales y Agrobiología de Sevilla (IRNAS), Consejo Superior de Investigaciones Científicas
(CSIC), Avda. Reina Mercedes 10, 41012 Sevilla, Spain
| | - Ángeles Prieto-Fernández
- Instituto
de Investigaciones Agrobiológicas de Galicia (IIAG), Consejo Superior de Investigaciones Científicas
(CSIC), Avda. de Vigo s/n, 15705 Santiago de Compostela, Spain
| | - Leslie M. Shor
- Department
of Chemical and Biomolecular Engineering, University of Connecticut, Castleman Building Rm. 224, Connecticut 06269-3237 Storrs, United States
| | - Subhasis Ghoshal
- Department
of Civil Engineering, McGill University, 817 Sherbrooke Street West, Montreal, Quebec H3A 0C3, Canada
| | | | - José Julio Ortega-Calvo
- Instituto
de Recursos Naturales y Agrobiología de Sevilla (IRNAS), Consejo Superior de Investigaciones Científicas
(CSIC), Avda. Reina Mercedes 10, 41012 Sevilla, Spain
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14
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Richter F, Bindschedler S, Calonne-Salmon M, Declerck S, Junier P, Stanley CE. Fungi-on-a-Chip: microfluidic platforms for single-cell studies on fungi. FEMS Microbiol Rev 2022; 46:6674677. [PMID: 36001464 PMCID: PMC9779915 DOI: 10.1093/femsre/fuac039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/11/2022] [Accepted: 08/22/2022] [Indexed: 01/07/2023] Open
Abstract
This review highlights new advances in the emerging field of 'Fungi-on-a-Chip' microfluidics for single-cell studies on fungi and discusses several future frontiers, where we envisage microfluidic technology development to be instrumental in aiding our understanding of fungal biology. Fungi, with their enormous diversity, bear essential roles both in nature and our everyday lives. They inhabit a range of ecosystems, such as soil, where they are involved in organic matter degradation and bioremediation processes. More recently, fungi have been recognized as key components of the microbiome in other eukaryotes, such as humans, where they play a fundamental role not only in human pathogenesis, but also likely as commensals. In the food sector, fungi are used either directly or as fermenting agents and are often key players in the biotechnological industry, where they are responsible for the production of both bulk chemicals and antibiotics. Although the macroscopic fruiting bodies are immediately recognizable by most observers, the structure, function, and interactions of fungi with other microbes at the microscopic scale still remain largely hidden. Herein, we shed light on new advances in the emerging field of Fungi-on-a-Chip microfluidic technologies for single-cell studies on fungi. We discuss the development and application of microfluidic tools in the fields of medicine and biotechnology, as well as in-depth biological studies having significance for ecology and general natural processes. Finally, a future perspective is provided, highlighting new frontiers in which microfluidic technology can benefit this field.
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Affiliation(s)
- Felix Richter
- Department of Bioengineering, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Saskia Bindschedler
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Maryline Calonne-Salmon
- Laboratory of Mycology, Université catholique de Louvain, Place Croix du Sud 2, B-1348 Louvain-la-Neuve, Belgium
| | - Stéphane Declerck
- Laboratory of Mycology, Université catholique de Louvain, Place Croix du Sud 2, B-1348 Louvain-la-Neuve, Belgium
| | - Pilar Junier
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Claire E Stanley
- Corresponding author: Department of Bioengineering, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, United Kingdom. E-mail:
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15
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Abstract
Anoxic microsites arising in fungal biofilms may foster the presence of obligate anaerobes. Here, we analyzed whether and to which degree hyphae of Coprinopsis cinerea thriving in oxic habitats enable the germination, growth, and dispersal of the obligate anaerobic soil bacterium Clostridium acetobutylicum. Time-resolved optical oxygen mapping, microscopy, and metabolite analysis revealed the formation and persistence of anoxic circum hyphal niches, allowing for spore germination, growth, and fermentative activity of the obligate anaerobe in an otherwise inhabitable environment. Hypoxic liquid films containing 80% ± 10% of atmospheric oxygen saturation around single air-exposed hyphae thereby allowed for efficient clostridial dispersal amid spatially separated (>0.5 cm) anoxic sites. Hyphae hence may serve as good networks for the activity and spatial organization of obligate anaerobic bacteria in oxygenated heterogeneous environments such as soil.
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16
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Xiong BJ, Stanley CE, Dusny C, Schlosser D, Harms H, Wick LY. pH Distribution along Growing Fungal Hyphae at Microscale. J Fungi (Basel) 2022; 8:599. [PMID: 35736082 PMCID: PMC9224906 DOI: 10.3390/jof8060599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 02/06/2023] Open
Abstract
Creating unique microenvironments, hyphal surfaces and their surroundings allow for spatially distinct microbial interactions and functions at the microscale. Using a microfluidic system and pH-sensitive whole-cell bioreporters (Synechocystis sp. PCC6803) attached to hyphae, we spatially resolved the pH along surfaces of growing hyphae of the basidiomycete Coprinopsis cinerea. Time-lapse microscopy analysis of ratiometric fluorescence signals of >2400 individual bioreporters revealed an overall pH drop from 6.3 ± 0.4 (n = 2441) to 5.0 ± 0.3 (n = 2497) within 7 h after pH bioreporter loading to hyphal surfaces. The pH along hyphal surfaces varied significantly (p < 0.05), with pH at hyphal tips being on average ~0.8 pH units lower than at more mature hyphal parts near the entrance of the microfluidic observation chamber. Our data represent the first dynamic in vitro analysis of surface pH along growing hyphae at the micrometre scale. Such knowledge may improve our understanding of spatial, pH-dependent hyphal processes, such as the degradation of organic matter or mineral weathering.
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Affiliation(s)
- Bi-Jing Xiong
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Permoserstraβe 15, 04318 Leipzig, Germany; (B.-J.X.); (D.S.); (H.H.)
| | - Claire E. Stanley
- Department of Bioengineering, Imperial College of London, South Kensington Campus, London SW7 2AZ, UK;
| | - Christian Dusny
- Helmholtz Centre for Environmental Research-UFZ, Department of Solar Materials, Permoserstraβe 15, 04318 Leipzig, Germany;
| | - Dietmar Schlosser
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Permoserstraβe 15, 04318 Leipzig, Germany; (B.-J.X.); (D.S.); (H.H.)
| | - Hauke Harms
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Permoserstraβe 15, 04318 Leipzig, Germany; (B.-J.X.); (D.S.); (H.H.)
| | - Lukas Y. Wick
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Permoserstraβe 15, 04318 Leipzig, Germany; (B.-J.X.); (D.S.); (H.H.)
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17
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Microbial Involvement in the Bioremediation of Total Petroleum Hydrocarbon Polluted Soils: Challenges and Perspectives. ENVIRONMENTS 2022. [DOI: 10.3390/environments9040052] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Nowadays, soil contamination by total petroleum hydrocarbons is still one of the most widespread forms of contamination. Intervention technologies are consolidated; however, full-scale interventions turn out to be not sustainable. Sustainability is essential not only in terms of costs, but also in terms of restoration of the soil resilience. Bioremediation has the possibility to fill the gap of sustainability with proper knowledge. Bioremediation should be optimized by the exploitation of the recent “omic” approaches to the study of hydrocarburoclastic microbiomes. To reach the goal, an extensive and deep knowledge in the study of bacterial and fungal degradative pathways, their interactions within microbiomes and of microbiomes with the soil matrix has to be gained. “Omic” approaches permits to study both the culturable and the unculturable soil microbial communities active in degradation processes, offering the instruments to identify the key organisms responsible for soil contaminant depletion and restoration of soil resilience. Tools for the investigation of both microbial communities, their degradation pathways and their interaction, will be discussed, describing the dedicated genomic and metagenomic approaches, as well as the interpretative tools of the deriving data, that are exploitable for both optimizing bio-based approaches for the treatment of total petroleum hydrocarbon contaminated soils and for the correct scaling up of the technologies at the industrial scale.
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18
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Estoppey A, Weisskopf L, Di Francesco E, Vallat-Michel A, Bindschedler S, Chain PS, Junier P. Improved methods to assess the effect of bacteria on germination of fungal spores. FEMS Microbiol Lett 2022; 369:6553822. [PMID: 35325127 DOI: 10.1093/femsle/fnac034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/08/2021] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial-fungal interactions (BFI) play a major role on ecosystem functioning and might be particularly relevant at a specific development stage. For instance, in the case of biological control of fungal pathogens by bacteria, a highly relevant kind of BFI, in-vitro experiments often assess the impact of a bacterium on the inhibition of actively growing mycelia. However, this fails to consider other stages of plant infection such as the germination of a spore or a sclerotium. This study aims to present novel experimental platforms for in-vitro experiments with fungal spores, in order to assess the effect of bacteria on germination and fungal growth control, to recover the metabolites produced in the interaction, and to enhance direct visualisation of BFI. Botrytis cinerea, a phytopathogenic fungus producing oxalic acid (OA) as pathogenicity factor, was used as model. Given that oxalotrophic bacteria have been shown previously to control the growth of B. cinerea, the oxalotrophic bacteria Cupriavidus necator and Cupriavidus oxalaticus were used as models. The experiments performed demonstrated the suitability of the methods and confirmed that both bacteria were able to control the growth of B. cinerea, but only in media in which soluble OA was detected by the fungus. The methods presented here can be easily performed in any microbiology laboratory and are not only applicable to screen for potential biocontrol agents, but also to better understand BFI.
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Affiliation(s)
- Aislinn Estoppey
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Laure Weisskopf
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Eva Di Francesco
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Armelle Vallat-Michel
- Neuchâtel Platform of Analytical Chemistry, University of Neuchâtel, Neuchâtel, Switzerland
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Patrick S Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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19
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Liu C, Lin H, Li B, Dong Y, Qiu Y. Screening endophyte with capability to improve phytoremediation efficiency from hyperaccumulators: A novel and efficient microfluidic method. CHEMOSPHERE 2022; 286:131723. [PMID: 34426131 DOI: 10.1016/j.chemosphere.2021.131723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/25/2021] [Accepted: 07/28/2021] [Indexed: 06/13/2023]
Abstract
Screening endophyte is the most important but also difficult to achieve a successful application in endophyte assisted phytoremediation process. Traditional screening procedure faced certain limitations including long time, difficulty in ascertaining the optimum strain and insignificant promotion efficiency of the selected strain in application. In this study, a novel endophyte screening method was established using microfluidic technology, realizing the real time observation of plant root phenotyping and allowing simultaneous incubation of different endophyte-plant systems. Using this method within two weeks, showed that endophyte Bacillus paramycoides (PE1), which possessed the best capability to improve phytoremediation efficiency from hyperaccumulator P. acinosa was successfully screened by evaluating root growth rate and effluent heavy metal (HM) concentration. PE1 increased root growth rate by 54.31 % and reduced the Cd concentration of chip effluent by 46.33 %. The results were verified by pot experiment, which showed that with PE1 inoculation, the biomass of P. acinosa promoted 42.50 % and Cd removal efficiency increased 55.49 %. Besides, significant and positive correlations were observed among the phytoremediation indicators obtained from microfluidic and traditional method, indicating the feasibility of microfluidic method. Our research provided a new and efficient method for endophyte screening, which could give a better understanding of endophyte assisted phytoremediation technology of HM contaminated soil.
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Affiliation(s)
- Chenjing Liu
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China; Beijing Key Laboratory on Resource-Oriented Treatment of Industrial Pollutants, Beijing, 100083, PR China
| | - Hai Lin
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China; Beijing Key Laboratory on Resource-Oriented Treatment of Industrial Pollutants, Beijing, 100083, PR China.
| | - Bing Li
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China; Beijing Key Laboratory on Resource-Oriented Treatment of Industrial Pollutants, Beijing, 100083, PR China
| | - Yingbo Dong
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China; Beijing Key Laboratory on Resource-Oriented Treatment of Industrial Pollutants, Beijing, 100083, PR China
| | - Yong Qiu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, PR China.
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20
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Kerk YJ, Jameel A, Xing X, Zhang C. Recent advances of integrated microfluidic suspension cell culture system. ENGINEERING BIOLOGY 2021; 5:103-119. [PMID: 36970555 PMCID: PMC9996741 DOI: 10.1049/enb2.12015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 11/19/2022] Open
Abstract
Microfluidic devices with superior microscale fluid manipulation ability and large integration flexibility offer great advantages of high throughput, parallelisation and multifunctional automation. Such features have been extensively utilised to facilitate cell culture processes such as cell capturing and culturing under controllable and monitored conditions for cell-based assays. Incorporating functional components and microfabricated configurations offered different levels of fluid control and cell manipulation strategies to meet diverse culture demands. This review will discuss the advances of single-phase flow and droplet-based integrated microfluidic suspension cell culture systems and their applications for accelerated bioprocess development, high-throughput cell selection, drug screening and scientific research to insight cell biology. Challenges and future prospects for this dynamically developing field are also highlighted.
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Affiliation(s)
- Yi Jing Kerk
- Institute of Biochemical EngineeringDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
| | - Aysha Jameel
- Institute of Biochemical EngineeringDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
- MOE Key Laboratory of Industrial BiocatalysisDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
| | - Xin‐Hui Xing
- Institute of Biochemical EngineeringDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
- MOE Key Laboratory of Industrial BiocatalysisDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
- Center for Synthetic and Systems BiologyTsinghua UniversityBeijingChina
| | - Chong Zhang
- Institute of Biochemical EngineeringDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
- MOE Key Laboratory of Industrial BiocatalysisDepartment of Chemical Engineering, Tsinghua UniversityBeijingChina
- Center for Synthetic and Systems BiologyTsinghua UniversityBeijingChina
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21
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Arellano-Caicedo C, Ohlsson P, Bengtsson M, Beech JP, Hammer EC. Habitat geometry in artificial microstructure affects bacterial and fungal growth, interactions, and substrate degradation. Commun Biol 2021; 4:1226. [PMID: 34702996 PMCID: PMC8548513 DOI: 10.1038/s42003-021-02736-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 10/01/2021] [Indexed: 11/25/2022] Open
Abstract
Microhabitat conditions determine the magnitude and speed of microbial processes but have been challenging to investigate. In this study we used microfluidic devices to determine the effect of the spatial distortion of a pore space on fungal and bacterial growth, interactions, and substrate degradation. The devices contained channels differing in bending angles and order. Sharper angles reduced fungal and bacterial biomass, especially when angles were repeated in the same direction. Substrate degradation was only decreased by sharper angles when fungi and bacteria were grown together. Investigation at the cellular scale suggests that this was caused by fungal habitat modification, since hyphae branched in sharp and repeated turns, blocking the dispersal of bacteria and the substrate. Our results demonstrate how the geometry of microstructures can influence microbial activity. This can be transferable to soil pore spaces, where spatial occlusion and microbial feedback on microstructures is thought to explain organic matter stabilization.
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Affiliation(s)
| | - Pelle Ohlsson
- Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Martin Bengtsson
- Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Jason P Beech
- Division of Solid State Physics, Lund University, Lund, Sweden
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22
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Methods for Studying Bacterial–Fungal Interactions in the Microenvironments of Soil. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11199182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Due to their small size, microorganisms directly experience only a tiny portion of the environmental heterogeneity manifested in the soil. The microscale variations in soil properties constrain the distribution of fungi and bacteria, and the extent to which they can interact with each other, thereby directly influencing their behavior and ecological roles. Thus, to obtain a realistic understanding of bacterial–fungal interactions, the spatiotemporal complexity of their microenvironments must be accounted for. The objective of this review is to further raise awareness of this important aspect and to discuss an overview of possible methodologies, some of easier applicability than others, that can be implemented in the experimental design in this field of research. The experimental design can be rationalized in three different scales, namely reconstructing the physicochemical complexity of the soil matrix, identifying and locating fungi and bacteria to depict their physical interactions, and, lastly, analyzing their molecular environment to describe their activity. In the long term, only relevant experimental data at the cell-to-cell level can provide the base for any solid theory or model that may serve for accurate functional prediction at the ecosystem level. The way to this level of application is still long, but we should all start small.
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23
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Harting R, Nagel A, Nesemann K, Höfer AM, Bastakis E, Kusch H, Stanley CE, Stöckli M, Kaever A, Hoff KJ, Stanke M, deMello AJ, Künzler M, Haney CH, Braus-Stromeyer SA, Braus GH. Pseudomonas Strains Induce Transcriptional and Morphological Changes and Reduce Root Colonization of Verticillium spp. Front Microbiol 2021; 12:652468. [PMID: 34108946 PMCID: PMC8180853 DOI: 10.3389/fmicb.2021.652468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/26/2021] [Indexed: 11/13/2022] Open
Abstract
Phytopathogenic Verticillia cause Verticillium wilt on numerous economically important crops. Plant infection begins at the roots, where the fungus is confronted with rhizosphere inhabiting bacteria. The effects of different fluorescent pseudomonads, including some known biocontrol agents of other plant pathogens, on fungal growth of the haploid Verticillium dahliae and/or the amphidiploid Verticillium longisporum were compared on pectin-rich medium, in microfluidic interaction channels, allowing visualization of single hyphae, or on Arabidopsis thaliana roots. We found that the potential for formation of bacterial lipopeptide syringomycin resulted in stronger growth reduction effects on saprophytic Aspergillus nidulans compared to Verticillium spp. A more detailed analyses on bacterial-fungal co-cultivation in narrow interaction channels of microfluidic devices revealed that the strongest inhibitory potential was found for Pseudomonas protegens CHA0, with its inhibitory potential depending on the presence of the GacS/GacA system controlling several bacterial metabolites. Hyphal tip polarity was altered when V. longisporum was confronted with pseudomonads in narrow interaction channels, resulting in a curly morphology instead of straight hyphal tip growth. These results support the hypothesis that the fungus attempts to evade the bacterial confrontation. Alterations due to co-cultivation with bacteria could not only be observed in fungal morphology but also in fungal transcriptome. P. protegens CHA0 alters transcriptional profiles of V. longisporum during 2 h liquid media co-cultivation in pectin-rich medium. Genes required for degradation of and growth on the carbon source pectin were down-regulated, whereas transcripts involved in redox processes were up-regulated. Thus, the secondary metabolite mediated effect of Pseudomonas isolates on Verticillium species results in a complex transcriptional response, leading to decreased growth with precautions for self-protection combined with the initiation of a change in fungal growth direction. This interplay of bacterial effects on the pathogen can be beneficial to protect plants from infection, as shown with A. thaliana root experiments. Treatment of the roots with bacteria prior to infection with V. dahliae resulted in a significant reduction of fungal root colonization. Taken together we demonstrate how pseudomonads interfere with the growth of Verticillium spp. and show that these bacteria could serve in plant protection.
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Affiliation(s)
- Rebekka Harting
- Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Alexandra Nagel
- Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Kai Nesemann
- Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Annalena M Höfer
- Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Emmanouil Bastakis
- Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Harald Kusch
- Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-Universität Göttingen, Göttingen, Germany.,Department of Medical Informatics, University Medical Center, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Claire E Stanley
- Institute of Chemical and Bioengineering, ETH Zürich, Zurich, Switzerland
| | | | - Alexander Kaever
- Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Katharina J Hoff
- Institute of Mathematics and Computer Science, Universität Greifswald, Greifswald, Germany
| | - Mario Stanke
- Institute of Mathematics and Computer Science, Universität Greifswald, Greifswald, Germany
| | - Andrew J deMello
- Institute of Chemical and Bioengineering, ETH Zürich, Zurich, Switzerland
| | - Markus Künzler
- Institute of Microbiology, ETH Zürich, Zurich, Switzerland
| | - Cara H Haney
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
| | - Susanna A Braus-Stromeyer
- Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Gerhard H Braus
- Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-Universität Göttingen, Göttingen, Germany
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24
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Gimeno A, Stanley CE, Ngamenie Z, Hsung MH, Walder F, Schmieder SS, Bindschedler S, Junier P, Keller B, Vogelgsang S. A versatile microfluidic platform measures hyphal interactions between Fusarium graminearum and Clonostachys rosea in real-time. Commun Biol 2021; 4:262. [PMID: 33637874 PMCID: PMC7910300 DOI: 10.1038/s42003-021-01767-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 01/29/2021] [Indexed: 02/07/2023] Open
Abstract
Routinely, fungal-fungal interactions (FFI) are studied on agar surfaces. However, this format restricts high-resolution dynamic imaging. To gain experimental access to FFI at the hyphal level in real-time, we developed a microfluidic platform, a FFI device. This device utilises microchannel geometry to enhance the visibility of hyphal growth and provides control channels to allow comparisons between localised and systemic effects. We demonstrate its function by investigating the FFI between the biological control agent (BCA) Clonostachys rosea and the plant pathogen Fusarium graminearum. Microscope image analyses confirm the inhibitory effect of the necrotrophic BCA and we show that a loss of fluorescence in parasitised hyphae of GFP-tagged F. graminearum coincides with the detection of GFP in mycelium of C. rosea. The versatility of our device to operate under both water-saturated and nutrient-rich as well as dry and nutrient-deficient conditions, coupled with its spatio-temporal output, opens new opportunities to study relationships between fungi.
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Affiliation(s)
- Alejandro Gimeno
- Ecological Plant Protection in Arable Crops, Plant Protection, Agroscope, Zurich, Switzerland
- Molecular Plant Biology and Phytopathology, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Claire E Stanley
- Institute for Chemical and Bioengineering, ETH Zürich, Zürich, Switzerland.
- Plant-Soil Interactions, Agroecology and Environment Research Division, Agroscope, Zurich, Switzerland.
- Department of Bioengineering, Imperial College London, London, UK.
| | - Zacharie Ngamenie
- Ecological Plant Protection in Arable Crops, Plant Protection, Agroscope, Zurich, Switzerland
| | - Ming-Hui Hsung
- Plant-Soil Interactions, Agroecology and Environment Research Division, Agroscope, Zurich, Switzerland
| | - Florian Walder
- Plant-Soil Interactions, Agroecology and Environment Research Division, Agroscope, Zurich, Switzerland
| | - Stefanie S Schmieder
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Division of Gastroenterology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Pilar Junier
- Laboratory of Microbiology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Beat Keller
- Molecular Plant Biology and Phytopathology, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Susanne Vogelgsang
- Ecological Plant Protection in Arable Crops, Plant Protection, Agroscope, Zurich, Switzerland.
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25
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Baranger C, Fayeulle A, Le Goff A. Microfluidic monitoring of the growth of individual hyphae in confined environments. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191535. [PMID: 32968492 PMCID: PMC7481688 DOI: 10.1098/rsos.191535] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 08/05/2020] [Indexed: 06/11/2023]
Abstract
Soil fungi have the ability to form large mycelial networks. They rely on the resources available in the soil to produce biomass and are able to degrade complex biomolecules. Some of them can even degrade recalcitrant organic pollutants and are considered as promising candidates for soil bioremediation strategies. However, the success of this approach depends on the ability of fungi to colonize the soil matrix, where they encounter spatial and temporal variations of confinement, humidity and nutrient concentration. In this paper, we present a study of fungal growth at the scale of single hyphae in a microfluidic device, allowing fine control of nutrient and water supply. Time-lapse microscopy allowed simultaneous monitoring of the growth of dozens of hyphae of Talaromyces helicus, a soil isolate, and of the model fungus Neurospora crassa through parallel microchannels. The distributions of growth velocity obtained for each strain were compared with measurements obtained in macroscopic solid culture. For the two strains used in the study, confinement caused the growth velocity to drop in comparison with unconfined experiments. In addition, N. crassa was also limited in its growth by the nutrient supply, while the microfluidic culture conditions seemed better suited for T. helicus. Qualitative observations of fungi growing in microfluidic chambers without lateral confinement also revealed that side walls influence the branching behaviour of hyphae. This study is one of the first to consider the confinement degree within soil microporosities as a key factor of fungal growth, and to address its effect, along with physicochemical parameters, on soil colonization, notably for bioremediation purposes.
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Affiliation(s)
- Claire Baranger
- Université de technologie de Compiègne, ESCOM, TIMR (Integrated Transformations of Renewable Matter), Biomechanics and Bioengineering, Centre de recherche Royallieu - CS 60 319 - 60 203 Compiègne Cedex, France
| | - Antoine Fayeulle
- Université de technologie de Compiègne, ESCOM, TIMR (Integrated Transformations of Renewable Matter), Biomechanics and Bioengineering, Centre de recherche Royallieu - CS 60 319 - 60 203 Compiègne Cedex, France
| | - Anne Le Goff
- Université de technologie de Compiègne, CNRS, Biomechanics and Bioengineering, Centre de recherche Royallieu - CS 60 319 - 60 203 Compiègne Cedex, France
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26
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Horowitz LF, Rodriguez AD, Ray T, Folch A. Microfluidics for interrogating live intact tissues. MICROSYSTEMS & NANOENGINEERING 2020; 6:69. [PMID: 32879734 PMCID: PMC7443437 DOI: 10.1038/s41378-020-0164-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 03/10/2020] [Accepted: 03/12/2020] [Indexed: 05/08/2023]
Abstract
The intricate microarchitecture of tissues - the "tissue microenvironment" - is a strong determinant of tissue function. Microfluidics offers an invaluable tool to precisely stimulate, manipulate, and analyze the tissue microenvironment in live tissues and engineer mass transport around and into small tissue volumes. Such control is critical in clinical studies, especially where tissue samples are scarce, in analytical sensors, where testing smaller amounts of analytes results in faster, more portable sensors, and in biological experiments, where accurate control of the cellular microenvironment is needed. Microfluidics also provides inexpensive multiplexing strategies to address the pressing need to test large quantities of drugs and reagents on a single biopsy specimen, increasing testing accuracy, relevance, and speed while reducing overall diagnostic cost. Here, we review the use of microfluidics to study the physiology and pathophysiology of intact live tissues at sub-millimeter scales. We categorize uses as either in vitro studies - where a piece of an organism must be excised and introduced into the microfluidic device - or in vivo studies - where whole organisms are small enough to be introduced into microchannels or where a microfluidic device is interfaced with a live tissue surface (e.g. the skin or inside an internal organ or tumor) that forms part of an animal larger than the device. These microfluidic systems promise to deliver functional measurements obtained directly on intact tissue - such as the response of tissue to drugs or the analysis of tissue secretions - that cannot be obtained otherwise.
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Affiliation(s)
- Lisa F. Horowitz
- Department of Bioengineering, University of Washington, Seattle, WA 98195 USA
| | - Adán D. Rodriguez
- Department of Bioengineering, University of Washington, Seattle, WA 98195 USA
| | - Tyler Ray
- Department of Mechanical Engineering, University of Hawaiʻi at Mānoa, Honolulu, HI 96822 USA
| | - Albert Folch
- Department of Bioengineering, University of Washington, Seattle, WA 98195 USA
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27
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Microfluidic cultivation and analysis tools for interaction studies of microbial co-cultures. Curr Opin Biotechnol 2019; 62:106-115. [PMID: 31715386 DOI: 10.1016/j.copbio.2019.09.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 08/20/2019] [Accepted: 09/02/2019] [Indexed: 12/11/2022]
Abstract
Microbial consortia are fascinating yet barely understood biological systems with an elusive intrinsic complexity. Studying microbial consortia and the interactions of their members is of major importance for the understanding, engineering and control of synthetic and natural microbial consortia. Microfluidic cultivation and analysis devices are versatile tools for the study of microbial interactions at the single-cell level. While there is a vast amount of literature on microfluidics for the investigation of monocultures only few studies on co-cultures have been conducted in this context. Here we give an overview of different microfluidic single-cell cultivation tools for the analysis of microbial consortia with a focus on their physiology, growth dynamics and cellular interactions. Finally, central challenges and perspectives for the future application of microfluidic tools for microbial consortia investigations will be given.
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28
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Kjeldgaard B, Listian SA, Ramaswamhi V, Richter A, Kiesewalter HT, Kovács ÁT. Fungal hyphae colonization by Bacillus subtilis relies on biofilm matrix components. Biofilm 2019; 1:100007. [PMID: 33447794 PMCID: PMC7798453 DOI: 10.1016/j.bioflm.2019.100007] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/15/2019] [Accepted: 10/19/2019] [Indexed: 02/07/2023] Open
Abstract
Bacteria interact with their environment including microbes and higher eukaryotes. The ability of bacteria and fungi to affect each other are defined by various chemical, physical and biological factors. During physical association, bacterial cells can directly attach and settle on the hyphae of various fungal species. Such colonization of mycelia was proposed to be dependent on biofilm formation by the bacteria, but the essentiality of the biofilm matrix was not represented before. Here, we demonstrate that secreted biofilm matrix components of the soil-dwelling bacterium, Bacillus subtilis are essential for the establishment of a dense bacterial population on the hyphae of the filamentous black mold fungus, Aspergillus niger and the basidiomycete mushroom, Agaricus bisporus. We further illustrate that these matrix components can be shared among various mutants highlighting the community shaping impact of biofilm formers on bacteria-fungi interactions.
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Affiliation(s)
- Bodil Kjeldgaard
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Stevanus A Listian
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Valliyammai Ramaswamhi
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Anne Richter
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.,Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Heiko T Kiesewalter
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.,Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
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29
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Ghanem N, Stanley CE, Harms H, Chatzinotas A, Wick LY. Mycelial Effects on Phage Retention during Transport in a Microfluidic Platform. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:11755-11763. [PMID: 31532190 DOI: 10.1021/acs.est.9b03502] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Phages (i.e., viruses that infect bacteria) have been considered as good tracers for the hydrological transport of colloids and (pathogenic) viruses. However, little is known about interactions of phages with (fungal) mycelia as the prevalent soil microbial biomass. Forming extensive and dense networks, mycelia provide significant surfaces for phage-hyphal interactions. Here, for the first time, we quantified the mycelial retention of phages in a microfluidic platform that allowed for defined fluid exchange around hyphae. Two common lytic tracer phages (Escherichia coli phage T4 and marine phage PSA-HS2) and two mycelia of differing surface properties (Coprinopsis cinerea and Pythium ultimum) were employed. Phage-hyphal interaction energies were approximated by the extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) approach of colloidal interaction. Our data show initial hyphal retention of phages of up to ≈4 × 107 plaque-forming unit (PFU) mm-2 (≈2550 PFU mm-2 s-1) with a retention efficiency depending on the hyphal and, to a lesser extent, the phage surface properties. Experimental data were supported by XDLVO calculations, which revealed the highest attractive forces for the interaction between hydrophobic T4 phages and hydrophobic C. cinerea surfaces. Our data suggest that mycelia may be relevant for the retention of phages in the subsurface and need to be considered in subsurface phage tracer studies. Mycelia-phage interactions may further be exploited for the development of novel strategies to reduce or hinder the transport of undesirable (bio) colloidal entities in environmental filter systems.
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Affiliation(s)
- Nawras Ghanem
- Department of Environmental Microbiology , Helmholtz Centre for Environmental Research - UFZ , Permoserstraße 15 , 04318 Leipzig , Germany
| | - Claire E Stanley
- Agroecology and Environment Research Division , Agroscope , Reckenholzstrasse 191 , 8046 Zurich , Switzerland
| | - Hauke Harms
- Department of Environmental Microbiology , Helmholtz Centre for Environmental Research - UFZ , Permoserstraße 15 , 04318 Leipzig , Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig , Deutscher Platz 5e , 04103 Leipzig , Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology , Helmholtz Centre for Environmental Research - UFZ , Permoserstraße 15 , 04318 Leipzig , Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig , Deutscher Platz 5e , 04103 Leipzig , Germany
| | - Lukas Y Wick
- Department of Environmental Microbiology , Helmholtz Centre for Environmental Research - UFZ , Permoserstraße 15 , 04318 Leipzig , Germany
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30
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Uehling JK, Entler MR, Meredith HR, Millet LJ, Timm CM, Aufrecht JA, Bonito GM, Engle NL, Labbé JL, Doktycz MJ, Retterer ST, Spatafora JW, Stajich JE, Tschaplinski TJ, Vilgalys RJ. Microfluidics and Metabolomics Reveal Symbiotic Bacterial-Fungal Interactions Between Mortierella elongata and Burkholderia Include Metabolite Exchange. Front Microbiol 2019; 10:2163. [PMID: 31632357 PMCID: PMC6779839 DOI: 10.3389/fmicb.2019.02163] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/03/2019] [Indexed: 01/12/2023] Open
Abstract
We identified two poplar (Populus sp.)-associated microbes, the fungus, Mortierella elongata strain AG77, and the bacterium, Burkholderia strain BT03, that mutually promote each other’s growth. Using culture assays in concert with a novel microfluidic device to generate time-lapse videos, we found growth specific media differing in pH and pre-conditioned by microbial growth led to increased fungal and bacterial growth rates. Coupling microfluidics and comparative metabolomics data results indicated that observed microbial growth stimulation involves metabolic exchange during two ordered events. The first is an emission of fungal metabolites, including organic acids used or modified by bacteria. A second signal of unknown nature is produced by bacteria which increases fungal growth rates. We find this symbiosis is initiated in part by metabolic exchange involving fungal organic acids.
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Affiliation(s)
- Jessie K Uehling
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States.,Department of Biology, Duke University, Durham, NC, United States
| | - Matthew R Entler
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Hannah R Meredith
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States.,Department of Biomedical Engineering, Duke University, Durham, NC, United States
| | - Larry J Millet
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,The Bredesen Center, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Collin M Timm
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jayde A Aufrecht
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Gregory M Bonito
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Nancy L Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jessy L Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Genome Science & Technology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Genome Science & Technology, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Scott T Retterer
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Joseph W Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
| | | | - Rytas J Vilgalys
- Department of Biology, Duke University, Durham, NC, United States
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31
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Millet LJ, Aufrecht J, Labbé J, Uehling J, Vilgalys R, Estes ML, Miquel Guennoc C, Deveau A, Olsson S, Bonito G, Doktycz MJ, Retterer ST. Increasing access to microfluidics for studying fungi and other branched biological structures. Fungal Biol Biotechnol 2019; 6:1. [PMID: 31198578 PMCID: PMC6556955 DOI: 10.1186/s40694-019-0071-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/15/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Microfluidic systems are well-suited for studying mixed biological communities for improving industrial processes of fermentation, biofuel production, and pharmaceutical production. The results of which have the potential to resolve the underlying mechanisms of growth and transport in these complex branched living systems. Microfluidics provide controlled environments and improved optical access for real-time and high-resolution imaging studies that allow high-content and quantitative analyses. Studying growing branched structures and the dynamics of cellular interactions with both biotic and abiotic cues provides context for molecule production and genetic manipulations. To make progress in this arena, technical and logistical barriers must be overcome to more effectively deploy microfluidics in biological disciplines. A principle technical barrier is the process of assembling, sterilizing, and hydrating the microfluidic system; the lack of the necessary equipment for the preparatory process is a contributing factor to this barrier. To improve access to microfluidic systems, we present the development, characterization, and implementation of a microfluidics assembly and packaging process that builds on self-priming point-of-care principles to achieve "ready-to-use microfluidics." RESULTS We present results from domestic and international collaborations using novel microfluidic architectures prepared with a unique packaging protocol. We implement this approach by focusing primarily on filamentous fungi; we also demonstrate the utility of this approach for collaborations on plants and neurons. In this work we (1) determine the shelf-life of ready-to-use microfluidics, (2) demonstrate biofilm-like colonization on fungi, (3) describe bacterial motility on fungal hyphae (fungal highway), (4) report material-dependent bacterial-fungal colonization, (5) demonstrate germination of vacuum-sealed Arabidopsis seeds in microfluidics stored for up to 2 weeks, and (6) observe bidirectional cytoplasmic streaming in fungi. CONCLUSIONS This pre-packaging approach provides a simple, one step process to initiate microfluidics in any setting for fungal studies, bacteria-fungal interactions, and other biological inquiries. This process improves access to microfluidics for controlling biological microenvironments, and further enabling visual and quantitative analysis of fungal cultures.
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Affiliation(s)
- Larry J. Millet
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS 6445, Oak Ridge, TN 37831 USA
- The Bredesen Center, University of Tennessee-Knoxville, Knoxville, TN 37996 USA
| | - Jayde Aufrecht
- The Bredesen Center, University of Tennessee-Knoxville, Knoxville, TN 37996 USA
- The Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, PO Box 2008, MS 6445, Oak Ridge, TN 37831 USA
| | - Jessy Labbé
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS 6445, Oak Ridge, TN 37831 USA
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, TN 37996 USA
| | - Jessie Uehling
- Biology Department, Duke University, Box 90338, Durham, NC 27708 USA
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, CA 94703 USA
| | - Rytas Vilgalys
- Biology Department, Duke University, Box 90338, Durham, NC 27708 USA
| | - Myka L. Estes
- The Center for Neuroscience, University of California Davis, One Shields Avenue, Davis, CA 95618 USA
| | - Cora Miquel Guennoc
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS 6445, Oak Ridge, TN 37831 USA
- Institut national de la recherche agronomique (INRA), Centre INRA-Lorraine, 54280 Champenoux, France
| | - Aurélie Deveau
- Institut national de la recherche agronomique (INRA), Centre INRA-Lorraine, 54280 Champenoux, France
| | - Stefan Olsson
- Fujian Agricultural and Forestry University, Fuzhou City, 350002 Fujian Province China
| | - Gregory Bonito
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824 USA
| | - Mitchel J. Doktycz
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS 6445, Oak Ridge, TN 37831 USA
- The Bredesen Center, University of Tennessee-Knoxville, Knoxville, TN 37996 USA
| | - Scott T. Retterer
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS 6445, Oak Ridge, TN 37831 USA
- The Bredesen Center, University of Tennessee-Knoxville, Knoxville, TN 37996 USA
- The Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, PO Box 2008, MS 6445, Oak Ridge, TN 37831 USA
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32
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Stöckli M, Morinaka BI, Lackner G, Kombrink A, Sieber R, Margot C, Stanley CE, deMello AJ, Piel J, Künzler M. Bacteria‐induced production of the antibacterial sesquiterpene lagopodin B in
Coprinopsis cinerea. Mol Microbiol 2019; 112:605-619. [DOI: 10.1111/mmi.14277] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Martina Stöckli
- Institute of Microbiology, Department of Biology ETH Zurich Vladimir‐Prelog‐Weg 4 ZürichCH‐8093Switzerland
| | - Brandon I. Morinaka
- Institute of Microbiology, Department of Biology ETH Zurich Vladimir‐Prelog‐Weg 4 ZürichCH‐8093Switzerland
| | - Gerald Lackner
- Institute of Microbiology, Department of Biology ETH Zurich Vladimir‐Prelog‐Weg 4 ZürichCH‐8093Switzerland
| | - Anja Kombrink
- Institute of Microbiology, Department of Biology ETH Zurich Vladimir‐Prelog‐Weg 4 ZürichCH‐8093Switzerland
| | - Ramon Sieber
- Institute of Microbiology, Department of Biology ETH Zurich Vladimir‐Prelog‐Weg 4 ZürichCH‐8093Switzerland
| | - Céline Margot
- Institute of Microbiology, Department of Biology ETH Zurich Vladimir‐Prelog‐Weg 4 ZürichCH‐8093Switzerland
| | - Claire E. Stanley
- Institute for Chemical and Bioengineering ETH Zurich Vladimir‐Prelog‐Weg 1 Zürich CH‐8093Switzerland
| | - Andrew J. deMello
- Institute for Chemical and Bioengineering ETH Zurich Vladimir‐Prelog‐Weg 1 Zürich CH‐8093Switzerland
| | - Jörn Piel
- Institute of Microbiology, Department of Biology ETH Zurich Vladimir‐Prelog‐Weg 4 ZürichCH‐8093Switzerland
| | - Markus Künzler
- Institute of Microbiology, Department of Biology ETH Zurich Vladimir‐Prelog‐Weg 4 ZürichCH‐8093Switzerland
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33
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Ogawa M, Bisson LF, García-Martínez T, Mauricio JC, Moreno-García J. New insights on yeast and filamentous fungus adhesion in a natural co-immobilization system: proposed advances and applications in wine industry. Appl Microbiol Biotechnol 2019; 103:4723-4731. [PMID: 31079167 DOI: 10.1007/s00253-019-09870-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/18/2019] [Accepted: 04/24/2019] [Indexed: 11/29/2022]
Abstract
Fungi possess extraordinary strength in attachment to biotic and abiotic surfaces. This review focuses on adhesion mechanisms of yeast and filamentous fungi and the proposed combination of the adhesive forces of both organisms in an immobilization system called yeast biocapsules, whereby Saccharomyces cerevisiae cells are attached to the hyphae of Penicillium chrysogenum. The natural adherent properties of each organism, one multicellular and another unicellular, allow yeast to be fixated securely on the filamentous fungi and complete alcoholic fermentation. Following alcoholic fermentation, the hyphae become an inert support for yeast cells while maintaining shape and integrity. Biocapsules have been used successfully in both wine and bioethanol production. Investigation of the potential genes involved in fungal-yeast fusion suggests that natural hydrophobic interactions of both organisms play a major role. Analysis of the possible mechanisms involved in fungus and yeast adhesion, future perspectives on improving yeast immobilization, and proposed applications of the biocapsules are explored.
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Affiliation(s)
- Minami Ogawa
- Department of Microbiology, University of Córdoba, Córdoba, Spain.,Department of Viticulture and Enology, University of California, Davis, Davis, CA, USA
| | - Linda F Bisson
- Department of Viticulture and Enology, University of California, Davis, Davis, CA, USA
| | | | - Juan C Mauricio
- Department of Microbiology, University of Córdoba, Córdoba, Spain
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34
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Fourie R, Pohl CH. Beyond Antagonism: The Interaction Between Candida Species and Pseudomonas aeruginosa. J Fungi (Basel) 2019; 5:jof5020034. [PMID: 31010211 PMCID: PMC6617365 DOI: 10.3390/jof5020034] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/18/2019] [Accepted: 04/18/2019] [Indexed: 12/11/2022] Open
Abstract
There are many examples of the interaction between prokaryotes and eukaryotes. One such example is the polymicrobial colonization/infection by the various opportunistic pathogenic yeasts belonging to the genus Candida and the ubiquitous bacterium, Pseudomonas aeruginosa. Although this interaction has simplistically been characterized as antagonistic to the yeast, this review highlights the complexity of the interaction with various factors influencing both microbes. The first section deals with the interactions in vitro, looking specifically at the role of cell wall components, quorum sensing molecules, phenazines, fatty acid metabolites and competition for iron in the interaction. The second part of this review places all these interactions in the context of various infection or colonization sites, i.e., lungs, wounds, and the gastrointestinal tract. Here we see that the role of the host, as well as the methodology used to establish co-infection, are important factors, influencing the outcome of the disease. Suggested future perspectives for the study of this interaction include determining the influence of newly identified participants of the QS network of P. aeruginosa, oxylipin production by both species, as well as the genetic and phenotypic plasticity of these microbes, on the interaction and outcome of co-infection.
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Affiliation(s)
- Ruan Fourie
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein 9301, South Africa.
| | - Carolina H Pohl
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein 9301, South Africa.
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35
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Tayyrov A, Stanley CE, Azevedo S, Künzler M. Combining microfluidics and RNA-sequencing to assess the inducible defensome of a mushroom against nematodes. BMC Genomics 2019; 20:243. [PMID: 30909884 PMCID: PMC6434838 DOI: 10.1186/s12864-019-5607-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 03/14/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Fungi are an attractive source of nutrients for predators. As part of their defense, some fungi are able to induce the production of anti-predator protein toxins in response to predation. A previous study on the interaction of the model mushroom Coprinopsis cinerea by the fungivorous nematode Aphelenchus avenae on agar plates has shown that the this fungal defense response is most pronounced in the part of the mycelium that is in direct contact with the nematode. Hence, we hypothesized that, for a comprehensive characterization of this defense response, an experimental setup that maximizes the zone of direct interaction between the fungal mycelium and the nematode, was needed. RESULTS In this study, we conducted a transcriptome analysis of C. cinerea vegetative mycelium upon challenge with A. avenae using a tailor-made microfluidic device. The device was designed such that the interaction between the fungus and the nematode was confined to a specific area and that the mycelium could be retrieved from this area for analysis. We took samples from the confrontation area after different time periods and extracted and sequenced the poly(A)+ RNA thereof. The identification of 1229 differentially expressed genes (DEGs) shows that this setup profoundly improved sensitivity over co-cultivation on agar plates where only 37 DEGs had been identified. The product of one of the most highly upregulated genes shows structural homology to bacterial pore-forming toxins, and revealed strong toxicity to various bacterivorous nematodes. In addition, bacteria associated with the fungivorous nematode A. avenae were profiled with 16S rRNA deep sequencing. Similar to the bacterivorous and plant-feeding nematodes, Proteobacteria and Bacteroidetes were the most dominant phyla in A. avenae. CONCLUSIONS The use of a novel experimental setup for the investigation of the defense response of a fungal mycelium to predation by fungivorous nematodes resulted in the identification of a comprehensive set of DEGs and the discovery of a novel type of fungal defense protein against nematodes. The bacteria found to be associated with the fungivorous nematode are a possible explanation for the induction of some antibacterial defense proteins upon nematode challenge.
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Affiliation(s)
- Annageldi Tayyrov
- Institute of Microbiology, Department of Biology, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093 Zürich, Switzerland
| | - Claire E. Stanley
- Agroecology and Environment Research Division, Agroscope, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
| | - Sophie Azevedo
- Institute of Microbiology, Department of Biology, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093 Zürich, Switzerland
| | - Markus Künzler
- Institute of Microbiology, Department of Biology, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093 Zürich, Switzerland
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36
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Bui TT, Harting R, Braus-Stromeyer SA, Tran VT, Leonard M, Höfer A, Abelmann A, Bakti F, Valerius O, Schlüter R, Stanley CE, Ambrósio A, Braus GH. Verticillium dahliae transcription factors Som1 and Vta3 control microsclerotia formation and sequential steps of plant root penetration and colonisation to induce disease. THE NEW PHYTOLOGIST 2019; 221:2138-2159. [PMID: 30290010 DOI: 10.1111/nph.15514] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 09/26/2018] [Indexed: 06/08/2023]
Abstract
Verticillium dahliae nuclear transcription factors Som1 and Vta3 can rescue adhesion in a FLO8-deficient Saccharomyces cerevisiae strain. Som1 and Vta3 induce the expression of the yeast FLO1 and FLO11 genes encoding adhesins. Som1 and Vta3 are sequentially required for root penetration and colonisation of the plant host by V. dahliae. The SOM1 and VTA3 genes were deleted and their functions in fungus-induced plant pathogenesis were studied using genetic, cell biology, proteomic and plant pathogenicity experiments. Som1 supports fungal adhesion and root penetration and is required earlier than Vta3 in the colonisation of plant root surfaces and tomato plant infection. Som1 controls septa positioning and the size of vacuoles, and subsequently hyphal development including aerial hyphae formation and normal hyphal branching. Som1 and Vta3 control conidiation, microsclerotia formation, and antagonise in oxidative stress responses. The molecular function of Som1 is conserved between the plant pathogen V. dahliae and the opportunistic human pathogen Aspergillus fumigatus. Som1 controls genes for initial steps of plant root penetration, adhesion, oxidative stress response and VTA3 expression to allow subsequent root colonisation. Both Som1 and Vta3 regulate developmental genetic networks required for conidiation, microsclerotia formation and pathogenicity of V. dahliae.
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Affiliation(s)
- Tri-Thuc Bui
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, University of Goettingen and Goettingen Center for Molecular Biosciences (GZMB), Grisebachstr. 8, D-37077, Goettingen, Germany
| | - Rebekka Harting
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, University of Goettingen and Goettingen Center for Molecular Biosciences (GZMB), Grisebachstr. 8, D-37077, Goettingen, Germany
| | - Susanna A Braus-Stromeyer
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, University of Goettingen and Goettingen Center for Molecular Biosciences (GZMB), Grisebachstr. 8, D-37077, Goettingen, Germany
| | - Van-Tuan Tran
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, University of Goettingen and Goettingen Center for Molecular Biosciences (GZMB), Grisebachstr. 8, D-37077, Goettingen, Germany
- Department of Microbiology, Faculty of Biology, VNU University of Science, 334 Nguyen Trai, Thanh Xuan, 100000, Hanoi, Vietnam
| | - Miriam Leonard
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, University of Goettingen and Goettingen Center for Molecular Biosciences (GZMB), Grisebachstr. 8, D-37077, Goettingen, Germany
| | - Annalena Höfer
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, University of Goettingen and Goettingen Center for Molecular Biosciences (GZMB), Grisebachstr. 8, D-37077, Goettingen, Germany
| | - Anja Abelmann
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, University of Goettingen and Goettingen Center for Molecular Biosciences (GZMB), Grisebachstr. 8, D-37077, Goettingen, Germany
| | - Fruzsina Bakti
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, University of Goettingen and Goettingen Center for Molecular Biosciences (GZMB), Grisebachstr. 8, D-37077, Goettingen, Germany
| | - Oliver Valerius
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, University of Goettingen and Goettingen Center for Molecular Biosciences (GZMB), Grisebachstr. 8, D-37077, Goettingen, Germany
| | - Rabea Schlüter
- Imaging Center of the Department of Biology, University of Greifswald, D-17489, Greifswald, Germany
| | - Claire E Stanley
- Plant-Soil Interactions, Agroecology and Environment Research Division, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
| | - Alinne Ambrósio
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, University of Goettingen and Goettingen Center for Molecular Biosciences (GZMB), Grisebachstr. 8, D-37077, Goettingen, Germany
| | - Gerhard H Braus
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, University of Goettingen and Goettingen Center for Molecular Biosciences (GZMB), Grisebachstr. 8, D-37077, Goettingen, Germany
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Schmieder SS, Stanley CE, Rzepiela A, van Swaay D, Sabotič J, Nørrelykke SF, deMello AJ, Aebi M, Künzler M. Bidirectional Propagation of Signals and Nutrients in Fungal Networks via Specialized Hyphae. Curr Biol 2019; 29:217-228.e4. [PMID: 30612903 DOI: 10.1016/j.cub.2018.11.058] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 10/05/2018] [Accepted: 11/23/2018] [Indexed: 11/15/2022]
Abstract
Intercellular distribution of nutrients and coordination of responses to internal and external cues via endogenous signaling molecules are hallmarks of multicellular organisms. Vegetative mycelia of multicellular fungi are syncytial networks of interconnected hyphae resulting from hyphal tip growth, branching, and fusion. Such mycelia can reach considerable dimensions and, thus, different parts can be exposed to quite different environmental conditions. Our knowledge about the mechanisms by which fungal mycelia can adjust nutrient gradients or coordinate their defense response to fungivores is scarce, in part due to limitations in technologies currently available for examining different parts of a mycelium over longer time periods at the microscopic level. Here, we combined a tailor-made microfluidic platform with time-lapse fluorescence microscopy to visualize the dynamic response of the vegetative mycelium of a basidiomycete to two different stimuli. The microfluidic platform allows simultaneous monitoring at both the colony and single-hypha level. We followed the dynamics of the distribution of a locally administered nutrient analog and the defense response to spatially confined predation by a fungivorous nematode. Although both responses of the mycelium were constrained locally, we observed long-distance propagation for both the nutrient analog and defense response in a subset of hyphae. This propagation along hyphae occurred in both acropetal and basipetal directions and, intriguingly, the direction was found to alternate every 3 hr in an individual hypha. These results suggest that multicellular fungi have, as of yet, undescribed mechanisms to coordinate the distribution of nutrients and their behavioral response upon attack by fungivores.
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Affiliation(s)
- Stefanie S Schmieder
- Department of Biology, Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Claire E Stanley
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zürich, Zürich, Switzerland
| | - Andrzej Rzepiela
- Scientific Center for Optical and Electron Microscopy, ETH Zürich, Switzerland
| | - Dirk van Swaay
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zürich, Zürich, Switzerland
| | - Jerica Sabotič
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Simon F Nørrelykke
- Scientific Center for Optical and Electron Microscopy, ETH Zürich, Switzerland
| | - Andrew J deMello
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zürich, Zürich, Switzerland
| | - Markus Aebi
- Department of Biology, Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Markus Künzler
- Department of Biology, Institute of Microbiology, ETH Zürich, Zürich, Switzerland.
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38
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Deveau A, Bonito G, Uehling J, Paoletti M, Becker M, Bindschedler S, Hacquard S, Hervé V, Labbé J, Lastovetsky OA, Mieszkin S, Millet LJ, Vajna B, Junier P, Bonfante P, Krom BP, Olsson S, van Elsas JD, Wick LY. Bacterial-fungal interactions: ecology, mechanisms and challenges. FEMS Microbiol Rev 2018; 42:335-352. [PMID: 29471481 DOI: 10.1093/femsre/fuy008] [Citation(s) in RCA: 321] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 02/16/2018] [Indexed: 12/14/2022] Open
Abstract
Fungi and bacteria are found living together in a wide variety of environments. Their interactions are significant drivers of many ecosystem functions and are important for the health of plants and animals. A large number of fungal and bacterial families engage in complex interactions that lead to critical behavioural shifts of the microorganisms ranging from mutualism to antagonism. The importance of bacterial-fungal interactions (BFI) in environmental science, medicine and biotechnology has led to the emergence of a dynamic and multidisciplinary research field that combines highly diverse approaches including molecular biology, genomics, geochemistry, chemical and microbial ecology, biophysics and ecological modelling. In this review, we discuss recent advances that underscore the roles of BFI across relevant habitats and ecosystems. A particular focus is placed on the understanding of BFI within complex microbial communities and in regard of the metaorganism concept. We also discuss recent discoveries that clarify the (molecular) mechanisms involved in bacterial-fungal relationships, and the contribution of new technologies to decipher generic principles of BFI in terms of physical associations and molecular dialogues. Finally, we discuss future directions for research in order to stimulate synergy within the BFI research area and to resolve outstanding questions.
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Affiliation(s)
- Aurélie Deveau
- Université de Lorraine, INRA, UMR IAM, 54280 Champenoux, France
| | - Gregory Bonito
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Jessie Uehling
- Biology Department, Duke University, Box 90338, Durham, NC 27705, USA.,Plant and Microbial Biology, University of California, Berkeley, CA 94703, USA
| | - Mathieu Paoletti
- Institut de Biologie et Génétique Cellulaire, UMR 5095 CNRS et Université de Bordeaux, 1 rue Camille Saint-Saëns, 33077 Bordeaux cedex, France
| | - Matthias Becker
- IGZ, Leibniz-Institute of Vegetable and Ornamental Crops, 14979 Großbeeren, Germany
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
| | - Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Vincent Hervé
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland.,Laboratory of Biogeosciences, Institute of Earth Surface Dynamics, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Jessy Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Olga A Lastovetsky
- Graduate Field of Microbiology, Cornell University, Ithaca, NY 14853, USA
| | - Sophie Mieszkin
- Université de Lorraine, INRA, UMR IAM, 54280 Champenoux, France
| | - Larry J Millet
- Joint Institute for Biological Science, University of Tennessee, and the Biosciences Division of Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Balázs Vajna
- Department of Microbiology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
| | - Paola Bonfante
- Department of Life Science and Systems Biology, University of Torino, 10125 Torino, Italy
| | - Bastiaan P Krom
- Department of Preventive Dentistry, Academic Centre for Dentistry, G. Mahlerlaan 3004, 1081 LA, Amsterdam, The Netherlands
| | - Stefan Olsson
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University (FAFU), Fuzhou 350002, China
| | - Jan Dirk van Elsas
- Microbial Ecology group, GELIFES, University of Groningen, 9747 Groningen, The Netherlands
| | - Lukas Y Wick
- Helmholtz Centre for Environmental Research-UFZ, Department of Environmental Microbiology, Permoserstraße 15, 04318 Leipzig, Germany
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39
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Stanley CE, Shrivastava J, Brugman R, Heinzelmann E, Frajs V, Bühler A, van Swaay D, Grossmann G. Fabrication and use of the dual-flow-RootChip for the imaging of Arabidopsis roots in asymmetric microenvironments. Bio Protoc 2018; 8:e3010. [PMID: 34395800 DOI: 10.21769/bioprotoc.3010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/20/2018] [Accepted: 09/04/2018] [Indexed: 11/02/2022] Open
Abstract
This protocol provides a detailed description of how to fabricate and use the dual-flow-RootChip (dfRootChip), a novel microfluidic platform for investigating root nutrition, root-microbe interactions and signaling and development in controlled asymmetric conditions. The dfRootChip was developed primarily to investigate how plants roots interact with their environment by simulating environmental heterogeneity. The goal of this protocol is to provide a detailed resource for researchers in the biological sciences wishing to employ the dfRootChip in particular, or microfluidic devices in general, in their laboratory.
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Affiliation(s)
- Claire E Stanley
- Agroecology and Environment Research Division, Agroscope, Zürich, Switzerland
| | - Jagriti Shrivastava
- Centre for Organismal Studies (COS) Heidelberg, Universität Heidelberg, Heidelberg, Germany.,Heidelberg Biosciences International Graduate School of Heidelberg Molecular Life Sciences (HBIGS), Universität Heidelberg, Heidelberg, Germany
| | - Rik Brugman
- Centre for Organismal Studies (COS) Heidelberg, Universität Heidelberg, Heidelberg, Germany
| | - Elisa Heinzelmann
- Centre for Organismal Studies (COS) Heidelberg, Universität Heidelberg, Heidelberg, Germany
| | - Viktoria Frajs
- Centre for Organismal Studies (COS) Heidelberg, Universität Heidelberg, Heidelberg, Germany
| | - Andreas Bühler
- Agroecology and Environment Research Division, Agroscope, Zürich, Switzerland
| | - Dirk van Swaay
- Institute for Chemical and Bioengineering, ETH Zürich, Zürich, Switzerland
| | - Guido Grossmann
- Centre for Organismal Studies (COS) Heidelberg, Universität Heidelberg, Heidelberg, Germany.,CellNetworks-Cluster of Excellence, Universität Heidelberg, Heidelberg, Germany
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40
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Baveye PC, Otten W, Kravchenko A, Balseiro-Romero M, Beckers É, Chalhoub M, Darnault C, Eickhorst T, Garnier P, Hapca S, Kiranyaz S, Monga O, Mueller CW, Nunan N, Pot V, Schlüter S, Schmidt H, Vogel HJ. Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain. Front Microbiol 2018; 9:1929. [PMID: 30210462 PMCID: PMC6119716 DOI: 10.3389/fmicb.2018.01929] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 07/30/2018] [Indexed: 01/17/2023] Open
Abstract
Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the bulk, macroscopic parameters (e.g., granulometry, pH, soil organic matter, and biomass contents) commonly used to characterize soils provide insufficient information to describe quantitatively the activity of soil microorganisms and some of its outcomes, like the emission of greenhouse gasses. Clearly, new, more appropriate macroscopic parameters are needed, which reflect better the spatial heterogeneity of soils at the microscale (i.e., the pore scale) that is commensurate with the habitat of many microorganisms. For a long time, spectroscopic and microscopic tools were lacking to quantify processes at that scale, but major technological advances over the last 15 years have made suitable equipment available to researchers. In this context, the objective of the present article is to review progress achieved to date in the significant research program that has ensued. This program can be rationalized as a sequence of steps, namely the quantification and modeling of the physical-, (bio)chemical-, and microbiological properties of soils, the integration of these different perspectives into a unified theory, its upscaling to the macroscopic scale, and, eventually, the development of new approaches to measure macroscopic soil characteristics. At this stage, significant progress has been achieved on the physical front, and to a lesser extent on the (bio)chemical one as well, both in terms of experiments and modeling. With regard to the microbial aspects, although a lot of work has been devoted to the modeling of bacterial and fungal activity in soils at the pore scale, the appropriateness of model assumptions cannot be readily assessed because of the scarcity of relevant experimental data. For significant progress to be made, it is crucial to make sure that research on the microbial components of soil systems does not keep lagging behind the work on the physical and (bio)chemical characteristics. Concerning the subsequent steps in the program, very little integration of the various disciplinary perspectives has occurred so far, and, as a result, researchers have not yet been able to tackle the scaling up to the macroscopic level. Many challenges, some of them daunting, remain on the path ahead. Fortunately, a number of these challenges may be resolved by brand new measuring equipment that will become commercially available in the very near future.
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Affiliation(s)
- Philippe C. Baveye
- UMR ECOSYS, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, rance
| | - Wilfred Otten
- School of Water, Energy and Environment, Cranfield University, Cranfield, United Kingdom
| | - Alexandra Kravchenko
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - María Balseiro-Romero
- UMR ECOSYS, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, rance
- Department of Soil Science and Agricultural Chemistry, Centre for Research in Environmental Technologies, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Éléonore Beckers
- Soil–Water–Plant Exchanges, Terra Research Centre, BIOSE, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Maha Chalhoub
- UMR ECOSYS, INRA, Université Paris-Saclay, Thiverval-Grignon, France
| | - Christophe Darnault
- Laboratory of Hydrogeoscience and Biological Engineering, L.G. Rich Environmental Laboratory, Department of Environmental Engineering and Earth Sciences, Clemson University, Clemson, SC, United States
| | - Thilo Eickhorst
- Faculty 2 Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Patricia Garnier
- UMR ECOSYS, INRA, Université Paris-Saclay, Thiverval-Grignon, France
| | - Simona Hapca
- Dundee Epidemiology and Biostatistics Unit, School of Medicine, University of Dundee, Dundee, United Kingdom
| | - Serkan Kiranyaz
- Department of Electrical Engineering, Qatar University, Doha, Qatar
| | - Olivier Monga
- Institut de Recherche pour le Développement, Bondy, France
| | - Carsten W. Mueller
- Lehrstuhl für Bodenkunde, Technical University of Munich, Freising, Germany
| | - Naoise Nunan
- Institute of Ecology and Environmental Sciences – Paris, Sorbonne Universités, CNRS, IRD, INRA, P7, UPEC, Paris, France
| | - Valérie Pot
- UMR ECOSYS, INRA, Université Paris-Saclay, Thiverval-Grignon, France
| | - Steffen Schlüter
- Soil System Science, Helmholtz-Zentrum für Umweltforschung GmbH – UFZ, Leipzig, Germany
| | - Hannes Schmidt
- Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, Research Network ‘Chemistry meets Microbiology’, University of Vienna, Vienna, Austria
| | - Hans-Jörg Vogel
- Soil System Science, Helmholtz-Zentrum für Umweltforschung GmbH – UFZ, Leipzig, Germany
- Institute of Soil Science and Plant Nutrition, Martin Luther University of Halle-Wittenberg, Halle, Germany
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Bhatia SK, Bhatia RK, Choi YK, Kan E, Kim YG, Yang YH. Biotechnological potential of microbial consortia and future perspectives. Crit Rev Biotechnol 2018; 38:1209-1229. [PMID: 29764204 DOI: 10.1080/07388551.2018.1471445] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Design of a microbial consortium is a newly emerging field that enables researchers to extend the frontiers of biotechnology from a pure culture to mixed cultures. A microbial consortium enables microbes to use a broad range of carbon sources. It provides microbes with robustness in response to environmental stress factors. Microbes in a consortium can perform complex functions that are impossible for a single organism. With advancement of technology, it is now possible to understand microbial interaction mechanism and construct consortia. Microbial consortia can be classified in terms of their construction, modes of interaction, and functions. Here we discuss different trends in the study of microbial functions and interactions, including single-cell genomics (SCG), microfluidics, fluorescent imaging, and membrane separation. Community profile studies using polymerase chain-reaction denaturing gradient gel electrophoresis (PCR-DGGE), amplified ribosomal DNA restriction analysis (ARDRA), and terminal restriction fragment-length polymorphism (T-RFLP) are also reviewed. We also provide a few examples of their possible applications in areas of biopolymers, bioenergy, biochemicals, and bioremediation.
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Affiliation(s)
- Shashi Kant Bhatia
- a Department of Biological Engineering, College of Engineering , Konkuk University , Seoul , South Korea.,b Institute for Ubiquitous Information Technology and Application , Konkuk University , Seoul , South Korea
| | - Ravi Kant Bhatia
- c Department of Biotechnology , Himachal Pradesh University , Shimla , India
| | - Yong-Keun Choi
- a Department of Biological Engineering, College of Engineering , Konkuk University , Seoul , South Korea.,d Texas A&M AGRILIFE Research & Extension Center , Texas A&M University , Stephenville , TX , USA
| | - Eunsung Kan
- d Texas A&M AGRILIFE Research & Extension Center , Texas A&M University , Stephenville , TX , USA
| | - Yun-Gon Kim
- e Department of Chemical Engineering , Soongsil University , Seoul , South Korea
| | - Yung-Hun Yang
- a Department of Biological Engineering, College of Engineering , Konkuk University , Seoul , South Korea.,b Institute for Ubiquitous Information Technology and Application , Konkuk University , Seoul , South Korea
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Abstract
The ecological modes of fungi are shaped not only by their intrinsic features and the environment in which they occur, but also by their interactions with diverse microbes. Here we explore the ecological and genomic features of diverse bacterial endosymbionts-endohyphal bacteria-that together are emerging as major determinants of fungal phenotypes and plant-fungi interactions. We first provide a historical perspective on the study of endohyphal bacteria. We then propose a functional classification of three main groups, providing an overview of their genomic, phylogenetic, and ecological traits. Last, we explore frontiers in the study of endohyphal bacteria, with special attention to those facultative and horizontally transmitted bacteria that associate with some of the most diverse lineages of fungi. Overall, our aim is to synthesize the rich literature from nearly 50 years of studies on endohyphal bacteria as a means to highlight potential applications and new research directions.
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43
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Stanley CE, Shrivastava J, Brugman R, Heinzelmann E, van Swaay D, Grossmann G. Dual-flow-RootChip reveals local adaptations of roots towards environmental asymmetry at the physiological and genetic levels. THE NEW PHYTOLOGIST 2018; 217:1357-1369. [PMID: 29125191 DOI: 10.1111/nph.14887] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 10/11/2017] [Indexed: 05/06/2023]
Abstract
Roots grow in highly dynamic and heterogeneous environments. Biological activity as well as uneven nutrient availability or localized stress factors result in diverse microenvironments. Plants adapt their root morphology in response to changing environmental conditions, yet it remains largely unknown to what extent developmental adaptations are based on systemic or cell-autonomous responses. We present the dual-flow-RootChip, a microfluidic platform for asymmetric perfusion of Arabidopsis roots to investigate root-environment interactions under simulated environmental heterogeneity. Applications range from investigating physiology, root hair development and calcium signalling upon selective exposure to environmental stresses to tracing molecular uptake, performing selective drug treatments and localized inoculations with microbes. Using the dual-flow-RootChip, we revealed cell-autonomous adaption of root hair development under asymmetric phosphate (Pi) perfusion, with unexpected repression in root hair growth on the side exposed to low Pi and rapid tip-growth upregulation when Pi concentrations increased. The asymmetric root environment further resulted in an asymmetric gene expression of RSL4, a key transcriptional regulator of root hair growth. Our findings demonstrate that roots possess the capability to locally adapt to heterogeneous conditions in their environment at the physiological and transcriptional levels. Being able to generate asymmetric microenvironments for roots will help further elucidate decision-making processes in root-environment interactions.
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Affiliation(s)
- Claire E Stanley
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir-Prelog-Weg 1, 8093, Zürich, Switzerland
- Agroecology and Environment Research Division, Agroscope, Reckenholzstrasse 191, 8046, Zürich, Switzerland
| | - Jagriti Shrivastava
- Centre for Organismal Studies (COS) Heidelberg, Universität Heidelberg, 69120, Heidelberg, Germany
- Hartmut Hoffmann-Berling International Graduate School of Heidelberg Molecular Life Sciences (HBIGS), Universität Heidelberg, 69120, Heidelberg, Germany
| | - Rik Brugman
- Centre for Organismal Studies (COS) Heidelberg, Universität Heidelberg, 69120, Heidelberg, Germany
| | - Elisa Heinzelmann
- Centre for Organismal Studies (COS) Heidelberg, Universität Heidelberg, 69120, Heidelberg, Germany
| | - Dirk van Swaay
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir-Prelog-Weg 1, 8093, Zürich, Switzerland
| | - Guido Grossmann
- Centre for Organismal Studies (COS) Heidelberg, Universität Heidelberg, 69120, Heidelberg, Germany
- CellNetworks-Cluster of Excellence, Universität Heidelberg, 69120, Heidelberg, Germany
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Aleklett K, Kiers ET, Ohlsson P, Shimizu TS, Caldas VE, Hammer EC. Build your own soil: exploring microfluidics to create microbial habitat structures. ISME JOURNAL 2017; 12:312-319. [PMID: 29135971 PMCID: PMC5776464 DOI: 10.1038/ismej.2017.184] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 08/25/2017] [Accepted: 09/15/2017] [Indexed: 11/23/2022]
Abstract
Soil is likely the most complex ecosystem on earth. Despite the global importance and extraordinary diversity of soils, they have been notoriously challenging to study. We show how pioneering microfluidic techniques provide new ways of studying soil microbial ecology by allowing simulation and manipulation of chemical conditions and physical structures at the microscale in soil model habitats.
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Affiliation(s)
| | - E Toby Kiers
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Pelle Ohlsson
- Department of Biomedical Engineering, Lund University, Lund, Sweden
| | | | - Victor Ea Caldas
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,AMOLF Institute, Amsterdam, The Netherlands
| | - Edith C Hammer
- Department of Microbial Ecology, Lund University, Lund, Sweden
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Microbiome-on-a-Chip: New Frontiers in Plant–Microbiota Research. Trends Microbiol 2017; 25:610-613. [DOI: 10.1016/j.tim.2017.05.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 04/26/2017] [Accepted: 05/01/2017] [Indexed: 11/21/2022]
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46
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de Menezes AB, Richardson AE, Thrall PH. Linking fungal–bacterial co-occurrences to soil ecosystem function. Curr Opin Microbiol 2017; 37:135-141. [DOI: 10.1016/j.mib.2017.06.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 06/21/2017] [Indexed: 02/04/2023]
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Tauber JP, Schroeckh V, Shelest E, Brakhage AA, Hoffmeister D. Bacteria induce pigment formation in the basidiomyceteSerpula lacrymans. Environ Microbiol 2016; 18:5218-5227. [DOI: 10.1111/1462-2920.13558] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/25/2016] [Accepted: 09/27/2016] [Indexed: 01/23/2023]
Affiliation(s)
- James P. Tauber
- Department of Pharmaceutical Microbiology at the Leibniz Institute for Natural Product Research and Infection Biology (HKI); Friedrich Schiller University; Beutenbergstrasse 11a Jena 07745 Germany
| | - Volker Schroeckh
- Department of Molecular and Applied Microbiology; Leibniz Institute for Natural Product Research and Infection Biology (HKI); Jena Germany
| | - Ekaterina Shelest
- Research Group Systems Biology/Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute; Jena Germany
| | - Axel A. Brakhage
- Department of Molecular and Applied Microbiology; Leibniz Institute for Natural Product Research and Infection Biology (HKI); Jena Germany
- Microbiology and Molecular Biology; Friedrich Schiller University Jena; Germany
| | - Dirk Hoffmeister
- Department of Pharmaceutical Microbiology at the Leibniz Institute for Natural Product Research and Infection Biology (HKI); Friedrich Schiller University; Beutenbergstrasse 11a Jena 07745 Germany
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48
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Gallegos-Monterrosa R, Mhatre E, Kovács ÁT. Specific Bacillus subtilis 168 variants form biofilms on nutrient-rich medium. MICROBIOLOGY-SGM 2016; 162:1922-1932. [PMID: 27655338 DOI: 10.1099/mic.0.000371] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Bacillus subtilis is an intensively studied Gram-positive bacterium that has become one of the models for biofilm development. B. subtilis 168 is a well-known domesticated strain that has been suggested to be deficient in robust biofilm formation. Moreover, the diversity of available B. subtilis laboratory strains and their derivatives have made it difficult to compare independent studies related to biofilm formation. Here, we analysed numerous 168 stocks from multiple laboratories for their ability to develop biofilms in different set-ups and media. We report a wide variation among the biofilm-forming capabilities of diverse stocks of B. subtilis 168, both in architecturally complex colonies and liquid-air interface pellicles, as well as during plant root colonization. Some 168 variants are indeed unable to develop robust biofilm structures, while others do so as efficiently as the non-domesticated NCIB 3610 strain. In all cases studied, the addition of glucose to the medium dramatically improved biofilm development of the laboratory strains. Furthermore, the expression of biofilm matrix component operons, epsA-O and tapA-sipW-tasA, was monitored during colony biofilm formation. We found a lack of direct correlation between the expression of these genes and the complexity of wrinkles in colony biofilms. However, the presence of a single mutation in the exopolysaccharide-related gene epsC correlates with the ability of the stocks tested to form architecturally complex colonies and pellicles, and to colonize plant roots.
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Affiliation(s)
- Ramses Gallegos-Monterrosa
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Eisha Mhatre
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Ákos T Kovács
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
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Stöckli M, Lin CW, Sieber R, Plaza DF, Ohm RA, Künzler M. Coprinopsis cinerea intracellular lactonases hydrolyze quorum sensing molecules of Gram-negative bacteria. Fungal Genet Biol 2016; 102:49-62. [PMID: 27475110 DOI: 10.1016/j.fgb.2016.07.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 07/21/2016] [Accepted: 07/25/2016] [Indexed: 10/21/2022]
Abstract
Biofilm formation on fungal hyphae and production of antifungal molecules are strategies of bacteria in their competition with fungi for nutrients. Since these strategies are often coordinated and under control of quorum sensing by the bacteria, interference with this bacterial communication system can be used as a counter-strategy by the fungi in this competition. Hydrolysis of N-acyl-homoserine lactones (HSL), a quorum sensing molecule used by Gram-negative bacteria, by fungal cultures has been demonstrated. However, the enzymes that are responsible for this activity, have not been identified. In this study, we identified and characterized two paralogous HSL hydrolyzing enzymes from the coprophilous fungus Coprinopsis cinerea. The C. cinerea HSL lactonases belong to the metallo-β-lactamase family and show sequence homology to and a similar biochemical activity as the well characterized lactonase AiiA from Bacillus thuringiensis. We show that the fungal lactonases, similar to the bacterial enzymes, are kept intracellularly and act as a sink for the bacterial quorum sensing signals both in C. cinerea and in Saccharomyces cerevisiae expressing C. cinerea lactonases, due to the ability of these signal molecules to diffuse over the fungal cell wall and plasma membrane. The two isogenes coding for the C. cinerea HSL lactonases are arranged in the genome as a tandem repeat and expressed preferentially in vegetative mycelium. The occurrence of orthologous genes in genomes of other basidiomycetes appears to correlate with a saprotrophic lifestyle.
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Affiliation(s)
- Martina Stöckli
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland.
| | - Chia-Wei Lin
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland.
| | - Ramon Sieber
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland.
| | - David F Plaza
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland.
| | - Robin A Ohm
- Microbiology, Faculty of Science, Utrecht University, Padualaan 8, 3584 Utrecht, The Netherlands.
| | - Markus Künzler
- Institute of Microbiology, Department of Biology, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland.
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50
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Stanley CE, Grossmann G, i Solvas XC, deMello AJ. Soil-on-a-Chip: microfluidic platforms for environmental organismal studies. LAB ON A CHIP 2016; 16:228-41. [PMID: 26645910 DOI: 10.1039/c5lc01285f] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Soil is the habitat of countless organisms and encompasses an enormous variety of dynamic environmental conditions. While it is evident that a thorough understanding of how organisms interact with the soil environment may have substantial ecological and economical impact, current laboratory-based methods depend on reductionist approaches that are incapable of simulating natural diversity. The application of Lab-on-a-Chip or microfluidic technologies to organismal studies is an emerging field, where the unique benefits afforded by system miniaturisation offer new opportunities for the experimentalist. Indeed, precise spatiotemporal control over the microenvironments of soil organisms in combination with high-resolution imaging has the potential to provide an unprecedented view of biological events at the single-organism or single-cell level, which in turn opens up new avenues for environmental and organismal studies. Herein we review some of the most recent and interesting developments in microfluidic technologies for the study of soil organisms and their interactions with the environment. We discuss how so-called "Soil-on-a-Chip" technology has already contributed significantly to the study of bacteria, nematodes, fungi and plants, as well as inter-organismal interactions, by advancing experimental access and environmental control. Most crucially, we highlight where distinct advantages over traditional approaches exist and where novel biological insights will ensue.
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Affiliation(s)
- Claire E Stanley
- Institute of Chemical and Bioengineering, ETH Zürich, Vladimir-Prelog-Weg 1, 8093 Zürich, Switzerland.
| | - Guido Grossmann
- Cell Networks-Cluster of Excellence and Centre for Organismal Studies (COS) Heidelberg, Universität Heidelberg, 69120 Heidelberg, Germany
| | | | - Andrew J deMello
- Institute of Chemical and Bioengineering, ETH Zürich, Vladimir-Prelog-Weg 1, 8093 Zürich, Switzerland.
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